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Mark Wilkinson, of the Department of Zoology, The Natural History Museum, London, U.K. (marw  (at) nhm.ac.uk) has produced REDCON, version 3.0, a program to implement his method of reduced consensus trees. These find a tree with possibly fewer species that satisfies a strict or a majority rule consensus criterion. REDCON reads trees in PAUP* format. It is a DOS executable, and is available at his software Web site at http://www.nhm.ac.uk/zoology/external/mwphylogeny.htm.

Mark Wilkinson, of the Department of Zoology, The Natural History Museum, London, U.K. (marw  (at) nhm.ac.uk) has produced TAXEQ3, a program to carry out Safe Taxonomic Reduction, which means dropping some species to get a set whose phylogenetic relationships are less ambiguous. The method is described in a paper: Wilkinson, M. 1995. Coping with abundant missing entries in phylogenetic inference using parsimony. Systematic Biology 44: 501-514. TAXEQ3 is distributed as a DOS executable with documentation and sample data set from his software Web site at http://www.nhm.ac.uk/zoology/external/mwphylogeny.htm.

Lars Jermiin of the School of Biological Sciences of the University of Sydney, Australia (lars.jermiin  (at) usyd.edu.au) and Olena Anpilogova have produced TreeCons version 1.0. It generates a weighted consensus tree from trees obtained by maximum likelihood analysis, generates relative likelihood support on edges in this and other user-specified trees, and does the Kishino-Hasegawa test with any level of significance. It reads output files and tree files produced by some of the programs in PHYLIP, MOLPHY, fastDNAml and TrExMl. The output file from TreeCons is in a format that then is fed back into PHYLIP's program Consense. A number of weighting schemes to compute tree weights from their likelihoods are allowed. The weighting schemes and the underlying theory are described in a paper: Jermiin L. S., G. J. Olsen, K. L. Mengersen, and S. Easteal. 1997. Majority-rule consensus of phylogenetic trees obtained by maximum likelihood analysis. Molecular Biology and Evolution 14: 1296-1302. TreeCons is distributed as C source code. It is available, with documentation and sample input and output, from its web site at http://jcsmr.anu.edu.au/dmm/humgen/lars/treeconssub.htm.

Joseph Thorley of Treleaver, Mithian Downs, St. Agnes, Cornwall TR5 0PY, U.K. (joethorley  (at) bigfoot.com) and Rod Page of the University of Glasgow have written RadCon, version 1.1.6, a program to compute consensus trees, supertrees, measures of the shape of trees, and to rearrange trees. It can compute strict, semi-strict, Adams, and majority-rule consensus trees, Reduced consensus trees, MRP supertrees, Cladistic Information Content, Leaf Stability, and Double Decay Analysis. It can also measure the shape and resolution of trees, prune and regraft leaves, add outgroups, and reroot trees. It is described in a paper: Thorley, J. L. and R. D. M. Page. 2000. RadCon: Phylogenetic comparison and consensus. Bioinformatics 16: 486-487. RadCon is a MacOS executable for MacOS 7.5 or later. RadCon is available at its web site at http://web.onetel.com/~joethorley/radcon/radcon.html and its manual can also be downloaded or viewed from there.

Jeet Sukumaran of the Division of Herpetology of the University of Kansas Natural History Museum and Biodiversity Research Center at the University of Kansas, Lawrence, Kansas (jeetsukumaran (at) frogweb.org) distributes bootscore version 3.11, a program to compute bootstrap support from boostrap replicate trees and place them on a consensus tree. A platform-independent Python script maps non-parametric bootstrap support for clades onto a phylogenetic tree. It outputs a NEXUS/Newick treefile with the topology of the given tree and with clade support indicated by node labels or branch lengths. In its default bipartition-counting mode, it identifies all distinct bipartitions in the tree to be evaluated, and then scans through a file of bootstrap replicates to identify the percentage or proportional frequency of occurance of each of those bipartitions in each of the bootstrap trees. It can also operate in a clade-counting mode, in which it identifies all distinct monophyletic groups in the tree being assessed, and then counts the number of bootstrap trees in which that particular monophyletic group is recovered. It is available as a Python script. It can be downloaded from its web site at http://bootscore.sourceforge.net/

Vladimir Makarenkov (makarenv  (at) magellan.umontreal.ca) of the Departement d'Informatique of the Université du Québec à Montréal and the Département de Sciences Biologiques of the Université de Montréal, Québec has written a program to compute the Robinson and Foulds topological distance. This is a distance measure between trees, counting the numbers of branches on the two trees that have no counterpart on the other tree. The algorithm used is described in a paper: Makarenkov, V., and Leclerc, B. 2000. An optimal way to compare additive trees using circular orders. Journal of Computational Biology 7: 731-744. The program is available as C source code and as DOS executable and a Mac OS executable from its web site at http://www.bio.umontreal.ca/Casgrain/en/labo/robinson_foulds.html.

  Pere Puigbò Avalos of the Evolutionary Genomics Group, Biochemistry and Biotechnology Department of Rovira i Virgili University, Tarragona, Spain (ppuigbo (at) urv.cat) has produced TopD/fMts (TOPological Distance / From Multiple To Single), version 1.0, program to calculate distances between trees. TopD calculates distances between trees by the following methods: split distance. nodal distance, disagreement, taxa in common, and quartets distance. fMtS is used with it to subsample gene families to get trees with one copy per species. It is described in the paper: Puigbò P., S. Garcia-Vallvé and J. O. McInerney. 2007. TOPD/FMTS: a new software to compare phylogenetic trees. Bioinformatics, published online on April 25, 2007. It is available as Perl script. It can be downloaded from its web site at http://genomes.urv.es/topd/

Chris Creevey (chris.creevey  (at) may.ie) of the Bioinformatics and Pharmacogenomics Laboratory at National University of Ireland Maynooth has written Clann (the Irish word for "family") version 2.0.3, a program to computer supertrees. It implements most of the major supertree methods, including matrix representation by parsimony (MRP), methods involving distance matrices, quartets methods, and splits methods, and includes a bootstrap method that samples from among the input trees. Clann is described in a paper: Creevey, C. J. and J. O. McInerney. 2005. Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 21: 390-392. It is available as Windows, Mac OS X, and Linux executables from its web site at http://bioinf.may.ie/software/clann/.

Nicolas Salamin at the Department of Ecology and Evolution of the University of Lausanne, Switzerland has written SuperTree, a program to take a set of input trees and build a matrix representation of them that can be used to compute a supertree using the MRP (matrix representation by parsimony) method. The program does not do the parsimony reconstruction from this matrix itself. The options available are described in a paper: Salamin, N., T. R. Hodkinson, V. Savolainen. 2002. Building supertrees: An empirical assessment using the grass family (Poaceae). Systematic Biology 51: 136 - 150. SuperTree is a Java runtime executable which will work on Linux, Windows, and Mac OS X systems, as long as they have the Sun Java Runtime JRT system version 1.3 or greater. The Java source code can be obtained from Salamin, if desired, by contacting him by email. The program and its distribution are briefly described at Salamin's software web site at http://www2.unil.ch/phylo/software.html  The program can be obtained from Salamin by emailing him (wwwphylo (at) unil.ch).

Olaf Bininda-Emonds at Technische Universität München, Germany (Olaf.Bininda  (at)  tierzucht.tum.de) has produced a set of Perl scripts which, taken together, are a Supertree package which can make and examine supertrees using the program PAUP*. Although they are each downloadable separately, I will consider them here to be a single entity. They include, in rough order of the steps carried out:

• synonoTree.pl, which standardizes the taxon labels in a set of source trees according to a reference taxonomy.
• treePruner.pl, which takes a set of NEXUS-formatted trees and prunes them to the set of tips that they all have in common.
• SuperMRP.pl, which converts a NEXUS-formatted treefile into a NEXUS- formatted MRP (Matrix Representation by Parsimony) data set ready for analysis by PAUP*.
• QualiTree.pl, which calculates support for clades in a supertree relative to the clades in the source trees that made it up.
• ReverseMRP.pl which does the reverse, making the NEXUS MRP data set into a treefile of trees.

They are described in the papers:

• Bininda-Emonds, O. R. P. 2003. Novel versus unsupported clades: assessing the qualitative support for clades in MRP supertrees. Systematic Biology 52: 839-848.
• Bininda-Emonds, O.R.P., K.E. Jones, S.A. Price, M. Cardillo, R. Grenyer, and A. Purvis. 2004. Garbage in, garbage out: data issues in supertree construction. Pp. 267-280 in Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, ed. O. R. P. Bininda-Emonds. Computational Biology, volume 4. Kluwer Academic Publishers, Dordrecht, the Netherlands.
• Bininda-Emonds, O.R.P., R.M.D. Beck, and A. Purvis. 2005. Getting to the roots of matrix representation. Systematic Biology 54: 668-672.

  Rod Page of the Environmental and Evolutionary Biology of the Institute of Biomedical and Life Sciences, University of Glasgow, U.K. (r.page (at) bio.gla.ac.uk) has written Supertree version 0.3, for constructing supertrees. Supertree is an experimental command line program for constructing supertrees. It implements Semple and Steel's algorithm MinCutSupertree (original and a modified version due to Page), as well as MRP coding. It can also compute cluster graphs. It is described in the paper: Page, R. D. M. 2002. Modified MinCut supertrees. pp. 537-551 in Algorithms in Bioinformatics: Proceedings of the Second International Workshop, WABI 2002, Rome, Italy, September 17-21, 2002. Springer-Verlag, Heidelberg. It is available as C source code, Mac OS X PowerMac executables and Mac OS 9 executables. To compile the source code, one needs a copy of the GTL Graph Template Library, which must be installed before compiling. Supertree can be downloaded from its web site at http://darwin.zoology.gla.ac.uk/%7Erpage/supertree/

Duhong Chen of the Computational Biology Laboratory of the Department of Computer Science of Iowa State University (duhong (at) iastate.edu) has written HeuristicMRF2 (Matrix Representation with Flipping version 2), a program to construct supertrees by the MRF method. Matrix representation with flipping (MRF) starts with a Matrix Representation by Parsimony matrix. The binary MRP matrix from a rooted input tree may be transformed into a subset of the columns of a rooted supertree by changing some of the 0's to 1's and 1's to 0's. Each change in the character state is a flip, and the minimum number of flips needed to transform the input tree into a supertree is the flip distance. The MRF heuristic seeks the rooted supertree(s) that minimizes the total flip distance from all input trees. It searches for rooted trees, not unrooted trees. It is described in the paper: Chen, D., L. Diao, O. Eulenstein, D. Fernández-Baca, and M. J. Sanderson. 2003. Flipping: A supertree construction method. Pp. 135-160 in Bioconsensus., ed. M. F. Janowitz, F.-J. Lapointe, F. R. McMorris, B. Mirkin, and F. S. Roberts. DIMACS series in discrete mathematics and theoretical computer science, Volume 61. American Mathematical Society, Providence, Rhode Island. It is available as C++ source code. It can be downloaded from its web site at http://genome.cs.iastate.edu/CBL/download/

Raul Piaggio of the Computational Biology Laboratory, Department of Computer Science at Iowa State University, Ames, Iowa (rpiaggio (at) iastate.edu) has written Quartet Suite version 1.0, a set of programs for computing supertrees and also distances between trees from quartets. Quartet Suite is a set of four programs that take input trees, break them down into the set of quartets implied by each of them, and construct a supertree based on these quartets. They can also compute a distance between trees from the sets of quartets they imply. The methods are described in the paper: Willson, S.J. 1999. Building phylogenetic trees from quartets by using local inconsistency measures. Molecular Biology and Evolution 16: 685-693. It is available as C++ source code, Windows executables and Powermac Mac OS X executables. It can be downloaded from its web site at http://genome.cs.iastate.edu/CBL/download/

Duhong Chen, Oliver Eulenstein, and David Fernández-Baca of the Computational Biology Laboratory of the Department of Computer Science at Iowa State University, Ames, Iowa (duhong (at) iastate.edu) have released Rainbow version beta 1.2, a toolbox for phylogenetic supertree construction and analysis. Rainbow provides a user-friendly environment in which scientists can utilize tools for building and analyzing supertrees. Rainbow provides a graphic user interface (GUI) to construct supertrees using several different methods. Currently these include matrix representation with flipping (MRF) matrix representation with parsimony (MRP), and the modified Mincut algorithm (MMC). Rainbow also provides tools to analyze the quality of the inferred supertrees. The methods are described in the paper: Chen, D., L. Diao, O. Eulenstein, D. Fernández-Baca, and M. J. Sanderson. 2003. Flipping: A supertree construction method. Pages 135-160 in Bioconsensus, ed. M. F. Janowitz, F.-J. Lapointe, F. R. McMorris, B. Mirkin, and F. S. Roberts. Volume 61 in DIMACS series in discrete mathematics and theoretical computer science, American Mathematical Society, Providence, Rhode Island. It is available as C++ source code, Windows executables, Linux executables and Powermac Mac OS X executables. It can be downloaded from its web site at http://genome.cs.iastate.edu/CBL/download/

Vincent Ranwez, Vincent Berry, Alexis Criscuolo, Pierre-Henri Fabre, Sylvain Guillemot, Celine Scornavacca and Emmanuel Douzery of the Institut des Sciences de L'evolution and the LIRMM at the Université Montpellier II, France (vberry (at) lirmm.fr) have produced PhySIC (Phylogenetic Supertrees with Induction and non-Contradiction), a supertree program that uses an algorithm they developed. It carries out construction of supertrees using the non-contradiction property (PC) and the induction property (PI). The former requires that the supertree does not contain relationships that contradict one or a combination of the source topolo- gies, while the latter requires that all topological information contained in the supertree is present in a source tree or collectively induced by several source trees. The program also can collapse branches in the input trees that have bootstrap values that are smaller than a threshold set by the user. It is described in the paper: Ranwez, V., V. Berry, A. Criscuolo, P.H. Fabre, S. Guillemot, C. Scornavacca and E.J.P. Douzery. 2007. PhySIC: a veto supertree method with desirable properties. Systematic Biology 56 (5): 798-817. It is available as Linux executables and Intel Mac OS X executables. It can be downloaded from its web site at http://atgc.lirmm.fr/SuperTree/PhySIC/

Ahmed Moustafa of the Computational Genetics program at the University of Iowa, Iowa City, Iowa (ahmed (at) users.sourceforge.net) has written PhyloSort version 1.3, a Java tool for sorting phylogenies searching for user-specified subtrees that a particular monophyletic group. PhyloSort is for

• Searching for monophyletic relationship among groups of taxa.
• Filtering by bootstrap support values associated with the monophyletic clades.
• Filtering by tree complexity (number of taxa in a tree).
• Filtering by family complexity (number of genes per taxon in a tree).
• Clustering trees (genes) into tree clusters (gene families).
• Using a reference tree to taxonomically group (tree-format).

Ross Crozier (Ross.Crozier  (at) jcu.edu.au) of the School of Tropical Biology, James Cook University, Townsville, Australia and Paul-Michael Agapow of the Department of Biology of Imperial College at Silwood Park, U.K. (p.agapow  (at) ucl.ac.uk) have written CONSERVE, version 3.1.2, a 68k Macintosh program to use phylogenetic information to calculate biodiversity and test the feasability of conservation schemes. It measures the distinctiveness of species using genetic distances and also to test whether particular assemblages of populations preserve statistically significantly more biodiversity than other assemblages. Biodiversity is determined using GD (probability of more than one allele) or PD (length of evolutionary history) methods, from data in the form of unrooted trees produced in standard treefile format. It is available as a Macintosh executable for the 680x0 processor (and thus can run in emulation mode in Mac OS) in a self-extracting archive from its web site at http://www.bio.ic.ac.uk/evolve/software/conserve/index.html.

George Weiller, of the Genomic Interactions Group at the Research School of Biological Sciences of the Australian National University, Canberra (georg.weiller  (at) rsbs.anu.edu.au) has released TreeDis version 2.0. TreeDis finds the patristic distances (total length of branches between all pairs of taxa in a phylogeny. It takes as input the tree file in Newick standard form or in the format for NJTREE. It is distributed as a DOS executable (a C++ source code version can also be obtained from Weiller). It is available from its web site at http://www.rsbs.anu.edu.au/Products&Services/BiotechnologyTransferUnit/tredis.asp.

Nicolas Bortolussi, Eric Durand, Michael Blum, and Olivier François of the Institut d'Informatique et Mathématiques Appliquées in Grenoble, France (nicolas.bortolussi (at) imag.fr) have written apTreeshape (analyses of phylogenetic Treeshape), version 1.3.1, an R package for simulation and analysis of phylogenetic tree topologies using statistical indices . apTreeshape computes a variety of statistics and tests on tree shape. It is a companion library of the APE package. It provides additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access to public databases, and enables testing null models of macroevolution using corrected test statistics. Trees of class "phylo" (from the APE package) can be converted easily. It is available as an R package, Windows executables and Powermac Mac OS X executables. It can be downloaded from its web site at http://cran.r-project.org/src/contrib/Descriptions/apTreeshape.html

Andrew Purvis of the Department of Biology, Imperial College, Silwood Park, U.K. (a.purvis  (at) ic.ac.uk) and Andrew Rambaut (andrew.rambaut  (at) zoo.ox.ac.uk) of the Department of Zoology, University of Oxford, England, have written CAIC (Comparative Analysis of Independent Contrasts), version 2.6.9. It is a Macintosh Mac OS program that carries out the contrasts method but with some modifications by others to cope with lack of resolution of the phylogeny. It will run on Macintosh Mac OS, and is available free from CAIC's Web page http://www.bio.ic.ac.uk/evolve/software/caic/index.html. It is described in the paper by A. Purvis and A. Rambaut (1995) Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. Computer Applications in the Biosciences (CABIOS) 11: 247-251.

Emília Martins (emartins  (at) indiana.edu), of the Department of Biology of the University of Indiana, Bloomington, Indiana, has released version 4.6 of COMPARE, a package of programs for comparative methods analysis. COMPARE includes various programs for conducting statistical analyses of comparative data in a phylogenetic context. At the moment, it includes programs to compute independent contrasts, do spatial autocorrelation analyses, sum of squares parsimony, generate random data, trees and/or branch lengths, and various other things. COMPARE is written in Java and is available both as standalone Java (including source code) and also as a Compare server. It requires a Java runtime environment. COMPARE is available from its web site at http://compare.bio.indiana.edu/. Earlier Windows and Sun Solaris executables and C source code of COMPARE 3.1 are available from the COMPARE 3.1 web site at http://compare.bio.indiana.edu/indexV3.html.

Emília Martins (emartins  (at) indiana.edu), of the Department of Biology of the University of Indiana, Bloomington, Indiana, has written CMAP, the Comparative Method Analysis Package, for comparative methods analysis. This package was developed when she and Ted Garland were conducting the simulation study described in the paper: Martins, E. P. and T. Garland, Jr. 1991. Phylogenetic analyses of the correlated evolution of continuous characters: a simulation study. Evolution 45: 534-557. It can be used to estimate the correlation between two continuous characters measured in different species while taking phylogenetic information into account. Methods for doing so include several versions of Felsenstein's (1985) independent contrasts, and the sum-of-squared-changes parsimony algorithm. The programs in CMAP are described by Martins as "slow" and "unfriendly". The executables are available only for DOS machines. She is no longer developing this package, and is now concentrating her efforts on her other package COMPARE, which will be able to do everything that CMAP can. CMAP is available from its download area at http://compare.bio.indiana.edu/ftp/.

Patrik Lindenfors (Patrik.Lindenfors  (at) zoologi.su.se), of the Department of Zoology, Stockholm University Sweden, and the Department of Biology, University of Virginia, Charlottesville (Patrik.Lindenfors  (at) virginia.edu), has written CoSta version 1.03, a DOS program which carries out the Contingent States Test for the correlation of changes in two characters along a tree, which is described in the paper: Sillén-Tullberg, B. 1993. The effect of biased inclusion of taxa on the correlation between discrete characters in phylogenetic trees. Evolution 47: 1182-1191. The program reads MacClade data files, and also text files saved from MacClade. The program can be fetched at its Web site at http://www.zoologi.su.se/research/Lindenfors/CoSta.html.

Theodore Garland, Jr., of the Department of Biology of the University of California, Riverside (tgarland  (at) ucr.edu) and his colleagues (Jason A. Jones, Allan W. Dickermann, Peter E. Midford, and Ramon Diaz-Uriarte) have developed PDAP version 6.0, Phenotypic Diversity Analysis Programs, a series of DOS programs to perform various comparative analyses. At present, the following phylogenetically based statistical methods are included: independent contrasts, squared-change parsimony reconstructions of ancestral states and estimation of evolutionary correlations, and phylogenetic analysis of covariance via computer-simulated (Monte Carlo) null distributions. PDTREE can also read, write, and edit trees. PDAP distribution is described in a web page at http://www.biology.ucr.edu/people/faculty/Garland/PDAP.html. The original published description of PDAP is the paper: Garland, T., Jr., A. W. Dickerman, C. M. Janis, and J. A. Jones. 1993. Phylogenetic analysis of covariance by computer simulation. Systematic Biology 42:265-292. The methods used are described in a number of recent papers by these authors, including:

• Purvis, A., and T. Garland, Jr. 1993. Polytomies in comparative analyses of continuous characters. Systematic Biology 42: 569-575.
• Diaz-Uriarte, R., and T. Garland, Jr. 1996. Testing hypotheses of correlated evolution using phylogenetically independent contrasts: sensitivity to deviations from Brownian motion. Systematic Biology 45: 27-47.
• Garland, T., Jr, P. E. Midford, and A. R. Ives. 1999. An introduction to phylogenetically based statistical methods, with a new method for confidence intervals on ancestral states. American Zoologist 39: 374-388.
• Garland, T., Jr., and A. R. Ives. 2000. Using the past to predict the present: Confidence intervals for regression equations in phylogenetic comparative methods. American Naturalist 155:346-364.

Liam Revell of the Department of Organismic and Evolutionary Biology of Harvard University (lrevell (at) fas.harvard.edu) has released IDC (IndepenDent Contrasts program), version 1, a program for the calculation of phylogenetically indepedent contrasts. This program calculates contrasts for multiple trees, multiple datasets, or both. It also returns a VCV matrix and the correlation matrix of the independent contrasts. It is available as C source code and Windows executables. It can be downloaded from its web site at http://anolis.oeb.harvard.edu/~liam/programs/

David Ackerly (dackerly  (at) stanford.edu) of the Department of Biological Sciences, Stanford University, Stanford, California has released ACAP 2 (Another Comparative Analysis Program) to carry out independent contrasts methods for comparative analysis. It also also incorporates linear parsimony methods into the program, in order to calculate consistency indices for continuous characters. The program is written in Think Pascal for Macintosh Mac OS systems, and is available from its web site at http://www.stanford.edu/~dackerly/ACAP.html as a Macintosh executable which will run on 68k Macintosh or PowerMacintosh Mac OS computers.

Ehab Abouheif (ehab.abouheif  (at) staff.mcgill.ca) of the Department of Biology, McGill University, Montréal, Québec has written (together with J. Reeve) Phylogenetic Independence version 2.0. It carries out Abouheif's Test For Serial Independence (TFSI) on continuously valued characters and his Runs Test on discretely valued characters. These are described in his paper: Abouheif, E. 1999. A method to test the assumption of phylogenetic independence in comparative data. Evolutionary Ecology Research 1: 895-909. The program is available as Windows and Linux executables at its web site at http://ww2.biology.mcgill.ca/biology/faculty/abouheif/programs.html.

Mark Pagel and Andrew Meade of the School of Biological Sciences, of the University of Reading, Reading, U.K. (m.pagel (at) reading.ac.uk) have released BayesTraits, a Bayesian package of programs to analyze state evolution of discrete and continuous traits. It is performs analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. It incoporates their earlier and separate programs Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a finite number of discrete states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits. Parts of the package are described in these papers:

• Pagel, M., A. Meade and D. Barker. 2004. Bayesian estimation of ancestral character states on phylogenies. Systematic Biology 53: 673-684.
• Pagel, M., and A.Meade. 2006. Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. American Naturalist 167: 808-825.
• Barker, D. and Pagel, M. 2005. Predicting functional gene links using phylogenetic-statistical analysis of whole genomes. PLoS Computational Biology 1: 24-31.

Aaron King and Marguerite Butler of the Department of Ecology and Evolutionary Biology of the University of Michigan, Ann Arbor, Michigan and the Department of Zoology of the Hawaii at Manoa (aaron.king (at) umich.edu and mbutler (at) hawaii.edu) have written OUCH (Ornstein-Uhlenbeck models models for phylogenetic Comparative Hypotheses), version 1.1-2, an R package using the Ornstein-Uhlenbeck model for comparative methods tests. The package fits different versions of Ornstein-Uhlenbeck models to comparative data, as described by Thomas Hansen. It is described in the paper: Butler, M. A. and A. A. King, 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist 164: 683-695. It is available as an R package, and requires the R statistical computing enironment to be available. It can be downloaded from its web site at http://tsuga.biology.lsa.umich.edu/king/ouch/

Chunghau Lee and Todd Oakley of the Ecology, Evolution and Marine Biology Department of the University of California at Santa Barbara, Santa Barbara, California (chunghaulee (at) gmail.com) and (oakley (at) lifesci.ucsb.edu) have released CoMET (COntinuous-character Model Evaluation and Testing), version of 081306, a Mesquite module for computing likelihoods for a given tree with Brownian motion models. COMet is a module for the Mesquite Project. Give it a tree topology as a starting point and some phenotypic data, and CoMET tells you the likelihoods of the data evolving through nine different evolutionary models, including both gradualist and punctuational models. It is described in the paper: Lee, C., S. Blay, A. Ø. Mooers, A. Singh, and T. H. Oakley. 2006. CoMET: A Mesquite package for comparing models of continuous character evolution on phylogenies. Evolutionary Bioinformatics Online 2: 193-196. CoMET requires the Mesquite Java framework for phylogenies. It is available as Java source code and Java executables. It can be downloaded from its web site at http://www.lifesci.ucsb.edu/eemb/labs/oakley/software/comet.htm

Brian O'Meara of the Center for Population Biology of the University of University of California, Davis. (bcomeara (at) ucdavis.edu) has released Brownie version 2.0, a program for analyzing rates of continuous character evolution. Brownie looks for substantial rate differences in different parts of a tree using likelihood ratio tests and Akaike Information Criterion (AIC) statistics. Brownie 2.0 can read Nexus tree and data files and can perform analyses across a set of weighted input trees (such as trees weighted by posterior probabilities or bootstrap values) in order to deal with tree uncertainty. Brownie deals with subtrees (using the censored test of O'Meara et al) and asks whether the subtrees differ in rates of evolution. An earlier version, Brownie 1.0, is written a series of MATLAB routines and can be used on systems that have MATLAB installed. It is described in the paper: O'Meara, B.C., C. Ané, M.J. Sanderson, and P.C. Wainwright. 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution 60(5): 922-933. It is available as C++ source code, Windows executables and Mac OS X universal executables. It can be downloaded from its web site at http://www.brianomeara.info/brownie/

Emanuel Paradis (paradis (at) isem.univ-montp2.fr) of the Institut des Sciences de l'Éolution of the Université Montpellier II and the CNRS, Montpellier, France has written APE, a package in the R statistical and graphical language which carries out a variety of phylogeny analyses, including computation of distances from sequences and gene frequencies, comparative methods, analyses of diversification, computation of minimum spanning trees, and estimation of rates of evolution and smoothing of rates in neighboring lineages. Some code was contributed by a number of other people, including Korbinian Strimmer, Julien Claude, Gangolf Jobb, Rainer Opgen-Rhein, Julien Dutheil, Yvonnick Noel, and Ben Bolker. APE is described in a paper: Paradis E., J. Claude and K. Strimmer. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290. R, a clone of the more commercialized S language, is available in Windows, Mac OS, and Linux versions. APE can be downloaded from its page atthe CRAN-R archive site of R programs at http://cran.r-project.org/src/contrib/Descriptions/ape.html; it is described and some additional documentation links given at its web site at http://pbil.univ-lyon1.fr/R/ape/

Ramón Díaz-Uriarte, of the Bioinformatics Unit of the Spanish National Cancer Center (CNIO), Madrid, Spain (rdiaz (at) ligarto.org) and Theodore Garland, Jr, of the Department of Biology of the University of California, Riverside (garland  (at) ucr.edu have released PHYLOGR, version 1.0.4. This is a package of programs in the R statistical language (and also available as a Windows executable) to carry out comparative methods analyses, particularly ones using the Generalized Least Squares method. The package is distributed through the web site of the Cran-R (Comprehensive R Archive Network) project at http://cran.r-project.org/src/contrib/Descriptions/PHYLOGR.html

Ted Garland of the Department of Biology of the University of California at Riverside (tgarland (at) citrus.ucr.edu) distributes PHYSIG (PHYlogenetic SIGnal), a MATLAB package of modules for comparative methods analysis. PHYSIG is a package of modules in MATLAB that includes tests for phylogenetic signal in continuous-character data, tests for the attraction to the mean in an Ornstein-Uhlenbeck model, and tests of evolutionary covariation between characters by a Generalized Least Squares method. It can be obtained by emailing Garland at the above address (it is not available by web download). The methods are described in the paper: Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57: 717-745. It is available as a MATLAB package, which can be downloaded from its web site at http://biology.ucr.edu/people/faculty/Garland/PHYSIG.html

Dylan Schwilk of the an ecologist with the Sequoia - Kings Canyon Research Station of the U. S. Geological Service (dylan (at) schwilk.org) has written Cactus-Pie (Python version of CACTUS: Comparative Analysis of Continuous Traits Using Statistics), version 0.3.1, a program for comparative analysis of continuous traits. Cactus-pie is a version of CACTUS written in Python. It consists of a front end program and a number of back-end modules. They include programs that calculate independent contrasts, provide the Divergence Order Test (DOT) and the Synchronized Changes Test (SvS), assign branch lengths to a phylogeny according to several different possible algorithms, and label clades in a phylogeny as defined by a taxa list in an auxilary file. It is available as Python script which can run on computers that have the Python language, which is widely available on Linux and Unix systems and is standard on Mac OS X. Cactus-Pie can be downloaded from its web site at http://www.pricklysoft.org/software/cactus-pie.html

Liam Revell of the Department of Organismic and Evolutionary Biology at Harvard University (lrevell (at) fas.harvard.edu) has released pcca (Phylogenetic Canonical Correlation Analysis), version Beta, a program for phylogenetic canonical correlation analysis. pcca uses a phylogenetic tree and measurements for an arbitrary number of continuous characters to perform a PGLS transformation of the data and then calculate canonical scores, weights, and correlations, and conduct hypothesis tests about the canonical correlations. Canonical correlation analysis (CCA) is a procedure using two sets of variables and calculating the linear combinations of each that have highest correlation with each other. The program can also estimate a multivariate version of Pagel's lambda transformation of time, and perform the analyses under that transformation. It is available as Windows executables, Linux executables and Mac OS X universal executables. It can be downloaded from its web site at http://anolis.oeb.harvard.edu/~liam/programs/

 David Posada (dposada  (at) uvigo.es), of the Universidad Vigo, Spain, and Taylor Maxwell and Alan Templeton, of the Department of Biology of Washington University, Saint Louis, Missouri (temple_a  (at) biology.wustl.edu) have written TreeScan, version 0.9. This is a program to test the association of continuous quantitative characters with a tree of haplottypes. It is described in a paper: Templeton, A. R., T. Maxwell, D. Posada, J. H. Stengård, . Boerwinkle, and C. F. Sing. 2005. Tree scanning: a method for using haplotype trees in phenotype/genotype association studies. Genetics 169: 441-453. Treescan is provided in C source code, and also as a DOS and Windows executable or a Mac OS X executable. It is available from its web site at http://darwin.uvigo.es/software/treescan.html

Dolph Schluter (schluter  (at) zoology.ubc.ca) of the Department of Zoology and Biodiversity Research Centre University of British Columbia, in Vancouver, Canada, has released ANCML, a program which estimates ancestor states for a continuous trait, and provides a "standard error" for the marginal distribution of each estimate. The method is described in Schluter, D., T. Price, A. Ø. Mooers and D. Ludwig. 1998. Likelihood of ancestor states in adaptive radiation. Evolution 51: 1699-1711. The method assumes a Brownian motion model for the evolution of the trait. ANCML was written by modifying the program CONTRAST in PHYLIP version 3.5, and it uses similar input conventions. ANCML is available from its web page at http://www.zoology.ubc.ca/~schluter/ancml.html. It is available as generic C source code and as a DOS executable.

Bill Bruno (billb  (at) lanl.gov) of the Theoretical Biology and Biophysics Group T10, Los Alamos Scientific Laboratory, has produced RIND, (Reconstructed INDependence), a program which takes a tree supplied by the user, or uses a distance method of the users choosing (one which can be found in PHYLIP), and computes a maximum likelihood estimate of the number of times each residue in aligned protein sequences was replaced in each position. The method is described in: Bruno, W. J. 1996, Modeling residue usage in aligned protein sequences via maximum likelihood Molecular Biology and Evolution 13: 1368-1374. RIND is available from its web site at http://www.t10.lanl.gov/billb/rind/ as C source code for a Unix environment, and assumes that PHYLIP is also installed.

Steve Woolley, then of the Department of Computer Science, Brigham Young University, Provo, Utah, together with Justin Johnson, Matthew Smith, Keith Crandall, and David McClellan of the Department of Integrative Biology (whose email address is David_McClellan  (at)  byu.edu) of that university have released TreeSAAP version 3.2, (Selection on Amino Acid Properties), a program that analyzes the frequency of change in various properties of amino acids in sequences evolving on well-corroborated phylogenies supplied by the user. TreeSAAP is given nucelotide sequences and a user-defined tree, and optimizes the placement of changes on the tree. It then calculates measure of departure of these changes from models of uniform neutral substitution, with respect to different properties of the amino acids. The methods are described in a paper: Woolley, S., J. Johnson, M. J. Smith, K. A. Crandall, and D. A. McClellan. 2003. TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees. Bioinformatics 19: 671-672. The program is a Java application. It is distributed as Windows executables, Mac OS X executables, and as Java source code from the McClellan lab software web site at http://inbio.byu.edu/faculty/dam83/cdm/

  Marcin Joachimiak (marcin  (at) compbio.berkeley.edu) of the Computational Genomics Research Group at University of California, Berkeley has released Jevtrace version 3.01. This is a Java package to analyze the distribution of amino acid changes across a phylogeny, and use protein structures to identify based on their distribution in the tree and in the protein structure. The program reads a multiple sequence alignment, a tree, and can also read a PDB protein structure. It displays the tree on either a branch length scale or a sequence similarity scale and allows the user to select clades of interest. The residues conserved in these clades and differing between them are then found and can then be viewed on the three-dimensional structure of the protein. Jevtrace is described in electronic publication: Joachimiak, M. P. and F. E. Cohen. 2003. JEvTrace: refinement and variations of the evolutionary trace in JAVA. Genome Biology 3 (12) http://genomebiology.com/2002/3/12/research/0077. The Jevtrace home page is available at http://www.cmpharm.ucsf.edu/~marcinj/JEvTrace/ at Fred Cohen's lab at University of California, San Francisco, where the program was written. The software cannot be directly downloaded from there: the user should fill out the Academic Software License form and submit it. Distribution is free for academic institutions (prices for others are not stated). The user will be emailed a link to download the software.

Xun Gu, of the Department of Genetics, Development and Cell Biology and the Center for Bioinformatics and Biological Statistics at Iowa State University, Ames, Iowa (xgu  (at) iastate.edu) and Kent Vander Velden, then at that University, have released DIVERGE version 1.04. DIVERGE reads protein sequences and either infers a tree by Neighbor-Joining or lets you read in a tree that you supply. It then allows you to define two clades in the tree, and tests whether the pattern of rates of change at different sites differ in these two clades. The statistical method used, which is a likelihood ratio test based in a probabilistic model, is given in the paper: Gu, X. 1999. Statistical methods for testing functional divergence after gene duplication. Molecular Biology and Evolution 16: 1664-1674. The program is downloadable as either Windows or Linux executables from the Gu laboratory software web site at http://xgu.zool.iastate.edu/software.html

Kent Fiala (fiala  (at) ipass.net) (most recently of SAS Institute) produced CLINCH (CLadistic INference by Compatibility of Hypothesized characters) version 6.2. It is a general-purpose compatibility program capable of handling multiple unordered states. It is available as a DOS executable, including FORTRAN source code, from the Digital Taxonomy web page at http://www.geocities.com/RainForest/Vines/8695/software.html#Cladistics.

Mark Wilkinson, of the Department of Zoology, The Natural History Museum, London, U.K. (marw  (at) nhm.ac.uk) has written PICA, version 4.0, a package of programs for character weighting and randomization tests for compatibility analysis for 0/1 or multistate characters. These carry out a variety of tests for nonrandomly compatible characters and include methods developed by Sharkey, Le Quesne, Meacham and Alroy. They include ability of process data that reflect the splits method of Bandelt and Dress. The programs are available as a package of DOS executables, from his software web site at http://www.nhm.ac.uk/research-curation/projects/software/mwphylogeny.html .

Christopher Meacham, affiliated with the University Herbarium, University of California, Berkeley produces COMPROB, a Pascal program to compute probabilities that characters would be compatible at random, thus telling us which clique is "most surprising". He can be contacted as meacham  (at) socrates.berkeley.edu about receiving a copy. The program is free.

John Armstrong, Adrian Gibbs, R. Peakall and George Weiller, (John.Armstrong  (at) anu.edu.au) of Mark Gibbs's group at the School of Botany and Zoology of the Australian National University, Canberra, have produced RAPDistance version 2.00, a package for DOS for computing distance matrices for RAPD analyses. Version 1.04 is also available, it has slightly more functionality but cannot handle data sets as large as version 2.00. RAPDistance has a comprehensive range of options for creating data files, editing them and using application programs to analyse them. It can export data sets in format of several other packages. RAPDistance is available free on the web at http://www.anu.edu.au/BoZo/software/index.html.

Peter Reeves and colleagues of the School of Molecular and Microbial Biosciences at Sydney University, Australia, have produced MULTICOMP, a program for computing various distances from sequence data. It can also do sequence format conversions, compute various descriptive statistics on the sequences, and can submit the sequences to two programs from PHYLIP. It is described in a paper: Reeves, P. R., L. Farnell and R. Lan. 1994. MULTICOMP: a program for preparing sequence data for phylogenetic analysis. Computer Applications in the Biosciences (CABIOS) 10: 281-284. I do not know what computer systems it runs on; perhaps it is a DOS program. Reeves may be contacted at reeves  (at) angis.usyd.oz.au for distribution information.

  Stuart Ray of the Division of Infectious Diseases at the Johns Hopkins University School of Medicine, Baltimore, Maryland (sray (at) jhmi.edu) have produced NimbleTree version 2.6, a program that submits data sets to PAUP* or PHYLIP. NimbleTree reads a variety of different sequence alignment formats, and allows you to more easily submit the resulting data sets to PHYLIP or to PAUP*. For PAUP* you need to have that program already installed on your computer. Some PHYLIP source code from its version 3.5p is included in NimbleTree (with my agreement). (I am not quite sure which methods from PHYLIP are available in this program). It is available as Windows executables. It can be downloaded from http://sray.med.som.jhmi.edu/SCRoftware/nimbletree/

Microsat, by Eric Minch, then of the Department of Human Genetics, Stanford University, Stanford, California (his email address is now eric.minch  (at) lionbioscience.com) is a program for calculating distances from microsatellite data. It uses the methods developed by David Goldstein et. al., and presented in their papers of 1995 in Proceedings of the Natonal Academy of Sciences USA 92: 6720-6727 and Genetics 139: 463-471. The distance is based on the mean microsatellite array size, implementing the "Δμ" distance that they defined, which corrects for within-population variability and provides a distance that is independent of population size. It is available for free from a page in Luca Cavalli-Sforza's lab web site at http://hpgl.stanford.edu/projects/microsat/. The program is written in ANSI C. Source code is distributed, and so are executables for DOS and Mac OS.

Daniel Dieringer (daniel.dieringer  (at) i122server.vu-wien.ac.at) and Christian Schlötterer of the University of Vienna have produced MSA (MicroSatellite Analyzer) version 3.15, a program for handling large microsatellite data sets. It can calculate many descriptive statistics for these data sets, can convert the data into a variety of file formats for other programs, and can also calculate a variety of distance measures. It is described in a paper: Dieringer, D., and C. Schlötterer. 2003. Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes 3: 167-169. MSA is available as source code in C plus executables for Linux, Windows (and DOS), Mac OS, and Mac OS X from its web site at http://i122server.vu-wien.ac.at/MSA/MSA_download.html.

Georg Weiller, of the Genomic Interactions Group at the Research School of Biological Sciences, Australian National University, Canberra, Australia (georg.weiller  (at) anu.edu.au) has produced DIPLOMO (DIstance PLOt MOnitor) version 1.03. It compares different distance measures with each other by displaying them as a scatter plot. It then helps one instantly identify all individual comparisons within the plot. individual taxa can be excluded or included in the plots, DIPLOMO enables you to see whether different taxa have different mutational characteristics (such as more having relatively more transitions in some lineages), and whether different distance measures correlate. The program takes as input a file with several different distance matrices. This file is in a simple format which can readily be produced by editing distance matrices produced by other packages. A program to compute the distance matrices is currently under development. Although DIPLOMO is intended to be ported to multiple platforms the current version runs on DOS on PC-compatibles. DIPLOMO is free; it can be obtained from its web site at http://life.anu.edu.au/molecular/software/diplomo/. It is described in a publication: Weiller, G. F. and A. Gibbs. 1995. DIPLOMO: The tool for a new type of evolutionary analysis. CABIOS 11: 535-40.

  Oclair Prado (oclair  (at) cpqd.com.br) and Fernando Van Zuben (vonzuben  (at)  dca.fee.unicamp.br) of the Department of Computer Science of the University of Campinas, Brazil released the Phylogenetic Tree Project (PTP) genetic algorithms toolbox, version 1.0. It infers phylogenies by maximum likelihood or a distance matrix method, using an evolutionary computation strategy which represents a phylogeny by a genotype, simulates natural selection to choose among phylogenies and recombination to rearrange phylogenies. It is a Windows executable, which can be downloaded by ftp from file PTP.zip at ftp.dca.fee.unicamp.br in folder /pub/docs/vonzuben/oclair.

Alan R. Lemmon (alemmon  (at) evotutor.org) and Michel Milinkovich (mcmilink  (at) ulb.ac.be) of the Unit of Evolutionary Genetics, Institute of Molecular Biology and Medicine, Free University of Brussels, Belgium have written MetaPIGA (Phylogeny Inference using the MetaGA), a program searching for maximum likelihood phylogenies using a genetic algorithm with metapopulations. This allows different populations in the genetic algorithm to arrive at different solutions, which can then be combined by migration and recombination. It is said to make possibe effective maximum likelihood inference of phylogenies for data sets with hundreds of species. MetaPIGA's approach is described in a paper: Lemmon, A. R. and M. C. Milinkovitch. 2001. The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation. Proceedings of the National Academy of Sciences, USA 99: 10516-10521. It is available as Java code from its web site at http://www.ulb.ac.be/sciences/ueg/html_files/MetaPIGA.html.

  Derrick Zwickl of the National Evolutionary Synthesis Center at Duke University, Durham, North Carolina (zwickl (at) nescent.org) released GARLI (Genetic Algorithm for Rapid Likelihood Inference), version 0.951, a program using a genetic algorithm to search for maximum likelihood phylogenies. GARLI uses a genetic algorithm to perform heuristic phylogenetic searches under the General Time Reversible (GTR) model of nucleotide substitution and its submodels, with or without gamma distributed rate heterogeneity and a proportion of invariant sites. Its likelihood computations are equivalent to those in PAUP*. It can read NEXUS and PHYLIP format sequence files. An MPI algorithm is included for use on parallel computing clusters (the parallel version seeks to perform a more thorough tree search and does not reduce runtimes. The program was written when Zwickl was a graduate student at the Department of Zoology of the University of Texas at Austin. It is described in his thesis: Zwickl, D. J. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, The University of Texas at Austin. It is available as C++ source code, Windows executables and Mac OS X universal executables. It can be downloaded from its web site at http://www.bio.utexas.edu/faculty/antisense/garli/Garli.html

MUST 2000, a package of sequence management programs, was developed by Hervé Philippe (herve.philippe (at) umontreal.ca), of the Departement de Biochimie Université de Montréal, Québec. It intended as complementary to existing phylogeny and alignment programs and can produce output files in the formats of PHYLIP, PAUP*, Hennig86, and CLUSTAL. It contains a variety of sequence input, editing, checking, and storage functions, as well as a sequence editor and a phylogeny plotter. It also allows further analyses of the results from these phylogeny programs. The original version of MUST is described in a paper: Philippe, H. 1993. MUST, a computer package of management utilities for sequences and trees. Nucleic Acids Research 21: 5264-5272. MUST 2000 is available as a Windows program from a download page at the University of Montpellier at http://www.isem.univ-montp2.fr/PPP/PM/RES/Info/@Softwares.php#MUST2000.

Steve Smith, formerly of the Harvard Genome Laboratory, has written an X-Windows interactive sequence editor, GDE (Genetic Data Environment), version 2.2, which allows the user to edit sequences and align them by hand, and to select subsets of sites and sequences and call a variety of analysis proprams including ClustalV and many of the PHYLIP 3.5 programs. The GDE 2.2 system will run on Unix or Linux systems using the X windowing system. It also includes the TreeTool tree-plotting program (see below). GDE has been described in two papers:

• Smith, S. W., R. Overbeek, C. R. Woese, W. Gilbert, and P. M. Gillevet. 1994. The genetic data environment an expandable GUI for multiple sequence analysis. Computer Applications in the Biosciences 10: 671-675.
• De Oliveira, T., R. Miller, M. Tarin, and S. Cassol. 2003. An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences. Bioinformatics 19: 153-154.

• At a web page at Michigan State University at http://www.msu.edu/~lintone/macgde/ MacGDE, is a MacOS X version that runs under X windows, ported by Tim Littlejohn (tim  (at) biolateralgroup.com) at BioLateral Group in Sydney, Australia.
• At the Bioafrica web site, a a download page http://www.bioafrica.net/GDElinux/index.html makes available GDElinux, the Linux port of GDE 2.2. It also has MacGDE available for download.

Brian Fristensky of the Department of Plant Science of the University of Manitoba, Winnipeg, Manitoba, Canada (frist (at) cc.umanitoba.ca) distributes BIRCH (BIological Research Computer Hierarchy), version 2.1, a sequence management and submission system with molecular databases. BIRCH consists of scripts and programs for a wide variety of analyses. It uses the GDE system for sequence editing and submission to programs. Some of the programs include many from PHYLIP, fastDNAml, Phylo_win, ATV, and ClustalW. BIRCH when installed also includes copies of molecular databases; the user is instructed on how to download these from their distribution sites. BIRCH is written in C and in Python and Java. It is distributed in source code and can be compiled on Linux and Solaris. The programs are distributed as binaries. The main BIRCH web site is at http://home.cc.umanitoba.ca/~psgendb/. It is described in the book chapter: Fristensky, B. 1999. Building a multiuser sequence analysis facility using freeware. pp 131-145 In S. Misener and S. A. Krawetz. Methods in Molecular Biology, vol. 132: Bioinformatics Methods and Protocols. Humana Press, Totowa, NJ, USA. BIRCH can be downloaded from its web site at http://www.umanitoba.ca/faculties/afs/plant_science/psgendb/FTP/BIRCH/download.html

Don Gilbert (gilbertd  (at) bio.indiana.edu) of the Department of Biology of the University of Indiana, has written SeqPup versions 0.9 and 0.6, a biological sequence editor and analysis program usable on MacOS, Windows and Unix systems. It allows alignment of sequences by hand and submission of selected parts of selected sequences to phylogeny programs, as well as to network services such as BLAST. It is available in a more complete earlier version (0.7) written in C++, or a later (0.9) version written in Java. The latter will work on all systems that have the Java 1.1 runtime environment. It will not work on the Java 1.2 runtime environment, so the earlier Java 1.1 environment needs to be installed as well if the later version of Java is present. (I do not know whether SeqPup works with later versions of Java). The two versions of SeqPup can be obtained a web page at iubio.bio.indiana.edu, if one follows the Local Reference link. or by World Wide Web at http://iubio.bio.indiana.edu/soft/molbio/seqpup. Versions 0.6 and 0.8 are also available by ftp from the software server at the Institut Pasteur at ftp.pasteur.fr in directory pub/GenSoft/Macintosh/sequence_tools/. GHE includes multiple sequence alignment with ClustalW, and phylogenetic analysis of alignments with the fastDNAml and LSADT programs. The earlier version (0.6) is available in C++, and executables of it are available for MacOS (the PowerMac and 68K platforms), Windows, and Unix X windows systems including Sun Solaris, SGI Irix, Dec (HP/Compaq) Unix, Linux. It is currently the more complete version, since it can also run some PHYLIP programs. The C++ source code for the earlier version available by anonymous ftp at: iubio.bio.indiana.edu in directory util/dclap/source/.

  Matthias Wolf, Joachim Friedrich, Thomas Dandekar, and Tobias Müller of the Department of Bioinformatics at the the Biocenter, University of Würzburg, Germany (joeMatthias.Wolf (at) biozentrum.uni-wuerzburg.de) have written CBCAnalyzer version 1.0.3, programs for inferring phylogenies based on compensatory base changes (CBCs). The CBCAnalyzer (CBC = compensatory base change) is a custom written software toolbox consisting of three parts, CTTransform, CBCDetect, and CBCTree. CTTransform reads several CT-file formats (ct, RNAviz ct or Mac ct), and generates a so called "bracket-dot-bracket" format that specifies which sites are paired in an RNA structure. This typically is used as input for other tools such as RNAforester, RNAmovie or MARNA. The latter one creates a multiple alignment based on primary sequences and secondary structures that now can be used as input for CBCDetect. The count (distance) matrix of compensating changes obtained by CBCDetect is used as input for CBCTree that reconstructs a phylogram by using the BIONJ algorithm. It is described in the paper: Wolf, M., J. Friedrich, T. Dandekar and T. Müller. 2005. CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures. In Silico Biology 5: 0027. It is available as C++ source code which can be compiled on Linux, and as Windows executables. It can be downloaded from its web site at http://cbcanalyzer.bioapps.biozentrum.uni-wuerzburg.de/

Wolfgang Ludwig and Oliver Strunk of the Lehrstuhl für Mikrobiologie of the Technische Universität München (wolfgang.ludwig  (at) biol.chemie.tu-muenchen.de) distribute ARB, an environment for 16s/18s/23s ribosomal RNA sequence data. It provides a windowing environment for building up databases of RNA sequences, aligning them, and searching, editing, modifying, aligning, profiling, and constructing trees. ARB uses its own RNA sequence databases which are made available to ARB over the Web. For phylogenies it uses programs from PHYLIP and fastDNAml, as well as its own ARB Neighbor-Joining program. ARB is also incorporates a variety of other sequence analysis software. It can handle large numbers of sequences and has sophisticated tree drawing and manipulation. ARB is distributed as executables for a variety of versions of Unix, requiring that the Motif library be available. At the moment these are: Solaris 5.x, SUN OS 4.1.x,, Silicon Graphics 5.0, Linux for PC, and Digital OSF. ARB is available from its web site at http://www.arb-home.de/ or by ftp from ftp://ftp.mpi-bremen.de/molecol_p/arb/. A Mac OS X port of ARB is available at the University of Melbourne at http://www.microbiol.unimelb.edu.au/micro/staff/mds/ARB_OSX/ARB_to_MacOSX.html.

Ian Holmes of the Department of Bioengineering of the University of California at Berkeley, Berkeley, Calfornia (ihh (at) berkeley.edu) has released DART (Dna, Amino and Rna Tests), a package of programs to do a variety of genomic, alignment, and RNA structure inferences. Various programs in the DART package do phylogenetic alignment; RNA structure prediction and multiple RNA alignment, stochastic grammars, inference of evolutionary models, phylo-HMMs and phylo grammars, reconstruction of ancestral sequences; and phylogenomics. It contains a number of programs including

• stemloc for RNA alignment
• xrate for phylo-grammars
• phylocomposer
• other statistical alignment programs in the Handel package

Andrew Smith, Thomas W. H. Lui and Elisabeth Tillier of the Ontario Cancer Institute and the Department of Medical Biophysics at the University of Toronto, Canada (e.tillier (at) utoronto.ca) have released rRNA phylogeny, a program package to infer phylogenies from ribosomal RNA using a model of substitution that allows for compensating substiutions at paired sites. The program makes use of a model (the OTRNA model) of ribosomal RNA substitution that has different rates for paired and unpaired sites, that reflect the lower probability of a compensated substitution that maintains the pairing. The model is empirically tabulated from rRNA sequences and used in a modified version of programs from PHYLIP to infer phylogenies. The package also allows distances to be computed from the OTRNA model for use in distance matrix programs. The methods are described in the paper: Smith, A., T. W. H. Lui and E. R. M. Tillier, 2004. Empirical substitution models for Ribosomal RNA Molecular Biology and Evolution 21: 419-427. It is available as C source code, Windows executables and Linux executables. It can be downloaded from its web site at http://www.uhnresearch.ca/labs/tillier/software.htm

Dick Hwang and Phil Green of the Department of Genome Sciences of the University of Washington, Seattle, Washington (dhwang (at) u.washington.edu) has released AMBIORE (Applications for Mcmc Bayesian Inference Of Rates in Evolution), version 1.00, which estimates rates of change in nucleotide sequences depending on the two neighboring bases.. It implements a flexible and computationally efficient Bayesian Markov chain Monte Carlo approach to estimating rates in evolution given a sequence alignment and tree topology relating the species. The evolutionary model allows substitution rates at a site to depend on the two flanking nucleotides, the branch of the phylogenetic tree, and position within a sequence. The methods are described in the paper: Hwang D. G. and P. Green. 2004. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proceedings of the National Academy of Sciences U.S.A. 101: 13994-14001. It is available as C source code. It can be downloaded from its web site at http://www.phrap.org/othersoftware.html

Henrik Nilsson and Bjørn Ursing of the Botanical Institute at the Gøteborg University and the Center for Genomics and Bioinformatics at the Karolinska Institute, Stockholm, Sweden (henrik.nilsson (at) botany.gu.se and bjorn.ursing (at) cgb.ki.se) have produced galaxie, a a package of CGI scripts for sequence identification through automated phylogenetic analysis. galaxie is a server, but also makes its scripts available for download. It is intended for identification of fungal EST sequences. It uses BLAST, ClustalW and PHYLIP to find a set of best matches to the EST sequence, then make a phylogeny of these matches and the original sequence to help identify the sequence. The CGI scripts require that the user who installs them be familiar with such scripts and have a web server, a and also have BLAST, ClustalW and PHYLIP installed on their computer. It is described in the paper: Nilsson, R. H., K.-B. Larsson, B. M. Ursing. 2004. galaxie - a CGI script package for sequence identification through automated phylogenetic analysis. Bioinformatics 20: 1447-1452. It is available as a package of Perl scripts. It can be downloaded from its web site at http://galaxie.cgb.ki.se/

Tom Hall of Ibis Therapeutics, Carlsbad, Calfornia (thall  (at) isisph.com) has produced BioEdit, version 7.0.9. This is a sequence editor with many kinds of general molecular biology functions available (alignment, BLAST searches, plasmid drawing, restriction mapping, sequence machine trace viewing, etc.). For our purposes the feature worth mentioning is that it comes with a number of existing phylogeny programs which can be automatically run from within BioEdit. These are: TreeView, fastDNAml, and six DNA and protein programs from PHYLIP. BioEdit is available as Windows95/98/NT executables from its web site at http://www.mbio.ncsu.edu/BioEdit/bioedit.html.

  GeneStudio, Inc. of Suwanee, Georgia (info  (at) genestudio.com) has released GeneStudio Pro a commercial package for sequence analysis and sequence format conversion. (Incidentally, although the Suwanee River is partly located in Georgia, the town of Suwanee is not located "way down upon the Suwanee River" but is quite far from it). Included is an Alignment Editor that can invoke a variety of phylogeny programs, including fastDNAml, some programs from PHYLIP, Tree-puzzle and TreeView. It can also do many other functions such as sequence format conversion, BLAST searches, and contig editing. GeneStudio Pro is for the Windows platform. A free trial version is available. Prices are not given on their web site but are available on request. For further information see the GeneStudio Pro web site at http://www.genestudio.com/genestudio.htm.

  Stuart Ray, of the Division of Infectious Diseases of the Department of Medicine at the Johns Hopkins University School of Medicine, Baltimore, Maryland (sray (at) jhmi.edu) has produced Simplot, version 3.5.1. It is a Windows program that serves as a front end to either code from PHYLIP or to PAUP* and enables you to easily submit jobs to them. SIMPLOT enables you to select regions and do other forms of data selection. It can also carry out the "bootscanning" method of detecting inconsistencies in trees in different regions of a sequence, which can be a signal for recombination. It is distributed as a Windows executable through its web site at http://sray.med.som.jhmi.edu/SCRoftware/simplot/

James J. Cai of the Department of Biology of Stanford University, Stanford, California (jamescai (at) stanford.edu) has written MBEToolbox (Molecular Biology and Evolution Toolbox), version 2.20, A MATLAB package to enable evolutionary biologists to analyze and view DNA and protein sequences. MBEToolbox includes sequence manipulation and statistics, evolutionary distance calculations, tree creation, a novel window analysis method and a graphical user interface. version 2.0 added new functions for phylogenetic analyses by the maximum likelihood method, analysis of site-specific evolutionary rates, and algorithms to detect recombination. It is described in the papers:

• Cai, J. J., D. K. Smith, X. Xia, and K.-Y. Yuen. 2005. MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution. BMC Bioinformatics 6: 64 (22Mar2005)
• Cai, J. J., D. K Smith, X. Xia, and K.-Y. Yuen. 2006. MBEToolbox 2.0: An enhanced version of a MATLAB toolbox for Molecular Biology and Evolution. Evolutionary Bioinformatics Online 2: 189-192.

Salvador Ramirez of the Departamento de Oceanografia of the Universidad de Concepcion, Chile (sram (at) profc.udec.cl) has released Bosque Phylogenetic Analysis Software, version 1.7.42, an integrated set of phylogenetic analysis software into a complete graphical user interface. Bosque is a graphical program that integrates console programs from the PHYLIP package, from TREE-PUZZLE, and from MUSCLE. As a graphical program it also includes sequence, alignment and tree editors to ease the manipulation of the data, the execution of the programs and the administration of the output result from the phylogenetic programs. It also has the option to function as a client-server program where a Bosque server is installed, thus allowing the remote execution of the mentioned phylogenetic programs. It is available as Windows executables and Linux executables. It can be downloaded from its web site at http://bosque.udec.cl

John Archibald and Andrew Roger, of the Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada (johna (at) hades.biochem.dal.ca and aroger (at) is.dal.ca) have released Likewind version 1.0. This is a set of three Perl scripts that allow the user to create the necessary PAUP* blocks to drive a likelihood analysis of differences in phylogenies betweend different parts of a molecule. The object is to detect recombination, hybridization, or other sources of conflicting phylogenetic signal. The utilities also harvest the output from PAUP* and present it to the user as a log-likelihood difference plot. This shows the log-likelihood difference in the window of adjacent sites between a predefined tree and the best estimate from the local information. The scripts need Seq-Gen and PAUP* present in a Linux environment. The method has been described in a paper: Archibald, J. M. and A. J. Roger. 2002. Gene conversion and the evolution of euryarchaeal chaperonins: a maximum likelihood-based method for detecting conflicting phylogenetic signals. Journal of Molecular Evolution 55: 232-245. Likewind is available from its web site at http://rogerlab.biochemistryandmolecularbiology.dal.ca/Software/Software.htm#likewind

Christian Zmasek, currently of the Genomics Institute of the Novartis Research Foundation in San Diego, California (czmasek  (at) gnf.org) and Sean Eddy (eddy  (at)  genetics.wustl.edu) of the Department of Genetics, Washington University, St. Louis, Missouri have released FORESTER, version 1.92, a package of Java routines for inferring gene function using the output of high-throughput genome sequencing. It includes the RIO Resampled Inference of Orthologs method which searches for orthologs in the PFAM database, the SDI Speciation-Duplication Inference method, and ATV, a tree viewer. This can take a tree in the standard Newick format (and also in an extension that has additional information), and display it in various forms. These are described in papers:

• Zmasek, C.M. and S. R. Eddy. 2001. ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics 17: 383-384.
• Zmasek, C. M. and S. R. Eddy. 2001. A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17: 821-828.
• Zmasek, C. M. and S. R. Eddy. 2002. RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics 3: 14.

Louxin Zhang (lxzhang  (at) krdl.org.sg) of the The Internet Bioinformatics Group of the Internet Research and Development Unit of the National University of Singapore has produced WebPHYLIP, a web interface for the PHYLIP package, which can submit jobs to it. It can be obtained by e-mailing him at the above address.

  Biomatters, Ltd. in Auckald, New Zealand (sales (at) geneious.com) has released Geneious version 2.53, a Java package for sequence management, searching, editing and phylogenies. Geneious is an integrated bioinformatics tool suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features tree-based progressive sequence alignment and phylogenetic analysis by Neighbor-Joining and UPGMA, bootstapping, drawing the phylogeny, access to biological databases, BLAST, protein structure viewing, NCBI, EMBL, PubMed auto-find, and more. It includes an API for creating your own plugins. It is available as Java executables. Geneious is available for free; that version cannot edit sequences or annotations, cannot run the multiple alignment program ClustalW from within Geneious, and cannot do some other tasks. A full version, Geneious Pro, is available commercially. Free downloads of Geneious or purchases of Geneious Pro can be done from the Biomatters web site at http://www.biomatters.com. Geneious Pro is available at a full price of $395 (and a student price of $175) from Biomatters, Ltd. Discount prices for multiuser licenses are also available. An additional plugin, MrBayesPlugin, enabling it to run MrBayes is available.

Catherine Letondal of the Institute Pasteur, Paris, France (letondal (at) pasteur.fr) distributes PISE (Pasteur Institute Software Environment), a tool to generate Web interfaces for Molecular Biology programs. PISE allows the user to generate web page interfaces to many programs, including PHYLIP and the EMBOSS package. Web interfaces for these are available in PISE. The web interfaces allow you to rapidly create a web server for running these programs. PISE is used to create the Pasteur Institute web server. PISE web servers allow the results of one program to the "piped" to another program. The web server generated is designed to be run on a Unix machine. It is described in the paper: Letondal C. 2001. A Web interface generator for molecular biology programs in Unix. Bioinformatics, 17(1): 73-82. It is available as Perl scripts. It can be downloaded from its web site at http://www.pasteur.fr/recherche/unites/sis/Pise/

The MathWorks of Natick, Massachusetts have produced Bioinformatics Toolbox version 3.1, a MATLAB toolbox for bioinformatics. It has many functions for sequence analysis and microarray data, including multiple sequence alignment and consensus sequences. For this listing, the relevant ones are that it enables you to create and edit phylogenetic trees. You can calculate pairwise distances between aligned or unaligned nucleotide or amino acid sequences using a broad range of similarity metrics, such as Jukes-Cantor, p-distance, alignment-score, or a user-defined distance method. Phylogenetic trees are constructed using hierarchical linkage with a variety of techniques, including neighbor joining, single and complete linkage, and UPGMA. Bioinformatics Toolbox includes tools for weighting and rerooting trees, calculating subtrees, and calculating canonical forms of trees. Through the graphical user interface, you can prune, reorder, and rename branches; explore distances; and read or write Newick-formatted files. You can also use the annotation tools in MATLAB to create presentation-quality trees. It is available as a MATLAB package. It is available from MathWorks, Inc. The price is not available on the website without a login, but there are Commercial, Academic, and Student prices. It us believed that commercial licenses are about $1,000, academic licenses about $90. More information and sales contact can be obtained from the product web site at http://www.mathworks.com/products/bioinfo/

  Andrew Rambaut of the Department of Zoology, University of Oxford, (andrew.rambaut  (at) zoo.ox.ac.uk) has written Bi-De version 0.1, to simulate the evolution of trees using various models of lineage birth and death, and sampling lineages from among those extant. It can simulate branching with or without regulation of the number of lineages. It also allows the user to specify the relationship between the number of lineages and the birth rate of lineages. The program is available free for MacOS system 7.0 or later, from its web page at the University of Oxford Zoology software site at http://evolve.zoo.ox.ac.uk/software.html?name=Bi-De. Its manual can also be viewed on-line at that site. Rambaut says that Bi-De is considered obsolete software, having been almost completely superseded by their later program Phyl-O-Gen.

 Andrew Rambaut, of the Department of Zoology, University of Oxford (andrew.rambaut  (at) zoo.ox.ac.uk) has written Phyl-O-Gen version 1.1, a tree simulation program. It simulates phylogenies produced by a birth-death process. It also has a mode that allows for multiple epdisodes of evolution and multiple mass extinctions. It is available as generic source code for Unix and as Mac OS, Mac OS X, and Windows executables. It is distributed from its web page at http://evolve.zoo.ox.ac.uk/software.html?id=phylogen. Although Rambaut considers it to supersede his earlier program Bi-De, my reading is that some features of the older program are not yet available in the newer one.

Oliver Pybus and Andrew Rambaut of the Department of Zoology, University of Oxford, (oliver.pybus  (at) zoo.ox.ac.uk and andrew.rambaut  (at) zoo.ox.ac.uk) has written Genie (GENealogical Interval Explorer) version 3.0, a program for the inference of demographic history from reconstructed phylogenies. The methods it implements are described in the papers:

• Pybus, O., A. Rambaut and P. Harvey. 2000. An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 155: 1429-1437.
• Pybus, O. G., M. A. Charleston, S. Gupta, A. Rambaut, E. C. Holmes, and P. H. Harvey. 2001. The epidemic behavior of the Hepatitis C Virus. Science 292: 2323-2325.
• Strimmer, K. and O. G. Pybus. 2001. Exploring the demographic history of DNA sequences using the generalised skyline plot. Molecular Biology and Evolution 18: 2298-2305.

Paul-Michael Agapow (p.agapow  (at) ic.ac.uk) and Nick Isaac, then of the Department of Biology, Imperial College, Silwood Park, U.K. has released MacroCAIC version 1.0.1, which was developed from CAIC, by Andy Purvis and Andrew Rambaut. MacroCAIC uses phylogenies and data sets of character values to examine correlates of species richness, i.e. which traits are associated with abnormal speciation. The phylogeny is used to make these correlations independent. Traits may be continuous or discrete, and not every trait value needs to be known for every clade in the phylogeny. MacroCAIC has been described in a paper: Agapow, P.-M. and N. J. B. Isaac. 2002. MacroCAIC: correlates of species richness. Diversity & Distributions 8: 41-43. MacroCAIC is a PowerMac and 68k Mac binary executable for Mac OS. It is available from its web site at http://www.bio.ic.ac.uk/evolve/software/macrocaic/index.html.

Andrew Rambaut of the Department of Zoology, University of Oxford, (andrew.rambaut  (at) zoo.ox.ac.uk) and Nick Grassly of the Department of Infectious Disease Epidemiology of Imperial College School of Medicine, St. Mary's Campus, London (n.grassly  (at) ic.ac.uk) have written Seq-Gen (Sequence Generator), version 1.3.2, a program that will simulate the evolution of nucleotide sequences and protein sequences along a phylogeny or multiple phylogenies, using common models of the nucleotide or protein substitution process. A range of models of molecular evolution are implemented Nucleotide frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. The models available are the Hasegawa, Kishino and Yano (HKY) model, the Felsenstein F84 model, the general reversible model, the Kimura 2-parameter model, the Jukes-Cantor model and the Dayhoff PAM, JTT, Blosum62, mtREV, and WAG amino acid substitution models. Rate heterogeneity among sites or among the different positions within a codon can be specified. Seq-Gen is described in a paper: Rambaut, A. and N. C. Grassly. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Computer Applications in the Biosciences ICABIOS) 13: 235-238. A Mac OS executable is available, as well as source code files for Unix systems. A Windows executable is available for an earlier version, 1.3.1. These are available from its Web page at http://evolve.zoo.ox.ac.uk/software.html?name=Seq-Gen.

  Tom Wilcox has written SG Runner version 2.0.1, a graphical user interface for running Seq-Gen. It is available as Powermac Mac OS X executables. It can be downloaded from his software web site at http://homepage.mac.com/tpwilcox/FileSharing15.html

Nick Grassly of the Department of Infectious Disease Epidemiology of Imperial College School of Medicine, St. Mary's Campus, London (n.grassly  (at) ic.ac.uk) and Andrew Rambaut of the Department of Zoology, University of Oxford, (andrew.rambaut  (at) zoo.ox.ac.uk) have written PSeq-Gen (Protein-Sequence Generator), version 1.0, which will simulate the evolution of protein sequences along evolutionary trees. Three common models of amino acid substitution are implemented (PAM, JTT, and mREV), allow for user-defined amino acid frequencies. Site-specific rate heterogeneity following a gamma distribution is allowed. The program can handle multiple trees and produce multiple data sets. PSeq-Gen is available from its Web site at http://evolve.zoo.ox.ac.uk/software.html?name=PSeq-Gen as Unix source code and also as Mac OS executables. An online manual can also be viewed at that site. PSeq-Gen is now largely superseded by Seq-Gen, and although its site still available it is not being actively supported at the Oxford site.

Nick Grassly (most recently of the Department of Biological Sciences at Imperial College, Silwood Park, U.K.) and Andrew Rambaut, of the Department of Zoology, University of Oxford (andrew.rambaut (at) zoo.ox.ac.uk) have released Treevolve, version 1.32 and also Ptreevolve, programs that simulate the evolution of DNA and protein sequences respectively. The molecular sequences are simulated under coalescent models with constant population size, or with exponential population size growth. In addition different levels of recombination can be specified. In Treevolve, it is also possible to have an island model of population subdivision. Treevolve and Ptreevolve are written in ANSI C and should compile on most Unix systems. They are also available as Mac OS executables, and a project file for the MetroWerks Codewarrior compiler is included in the Macintosh archive. They can be obtained, and the manual of the programs viewed, from their web site at http://evolve.zoo.ox.ac.uk/software.html?name=Treevolve.

Jens Stoye, Dirk Evers and Folker Meyer of the Research Center for Interdisciplinary Studies on Structure Formation (FSPM) and the Technische Fakultät of the University of Bielefeld, Germany (j.stoye  (at) dkfz-heidelberg.de, dirk  (at)  TechFak.Uni-Bielefeld.de, and folker  (at)  TechFak.Uni-Bielefeld.de) have released ROSE, the Random model Of Sequence Evolution, version 1.3. It simulates the evolution of DNA, RNA, or protein sequences on a randomly generated tree, allowing insertions and deletions and substitution at different rates at different sites as well. It can also use a predefined tree that is input in standard format. It can report ancestral sequences or sequences at the tips of the tree, and it also keeps a record of the true multiple sequence alignment for comparison with the results of multiple sequence alignment programs. ROSE is described in the paper: Stoye, J. D. Evers and F. Meyer. 1998. Rose: generating sequence families. Bioinformatics 14: 157-163. ROSE is available in source code at its web site at http://bibiserv.techfak.uni-bielefeld.de/rose/. Version 1.0 is also available as binary executables for SunOS and for SGI Unix by anonymous ftp from ftp.Uni-Bielefeld.de in directory pub/projects/techfak/pi/rose/. ROSE is also available as a server.

Lars Jermiin of the School of Biological Sciences of the University of Sydney, Australia (lars.jermiin  (at) usyd.edu.au) has written Hetero, version 1.0, a program to simulate evolution of DNA sequences on four-species trees. The program allows many different kinds of heterogeneity of processes and rates, including different models of change on different branches. It gives a number of different kinds of summaries of the properties of the resulting sequences, as well as writing them to files for use by other programs. It is described in a paper: Jermiin, L. S., S. Y. W. Ho, F. Ababneh, J. Robinson, and A. W. D. Larkum. 2003. Hetero: a program to simulate the evolution of DNA on a four-taxon tree. Applied Bioinformatics 2: 159-163. It is distributed as executables for Sun Solaris, for Windows, and for Mac OS X from its web site at http://www.bio.usyd.edu.au/~jermiin/hetero.htm. Source code is also offered to those users who obtain a license for use of source code from the book Numerical Recipes.

Andy Pang, Andrew Smith, Paulo Nuin and Elisabeth Tillier of the Cancer Genomics and Proteomics Division of the Ontario Cancer Institute and the Department of Medical Biophysics of the University of Toronto, Canada (e.tillier (at) utoronto.ca) have released Simprot (SIMulation of PROTeins), version 1.01, a program to simulate protein evolution by substitution, insertion and deletion. It allows for several models of amino acid substitution (PAM, JTT and PMB), it allows for gamma distributed sites rates according to Yang's model, and it implements a parameterised Qian and Goldstein distribution model for insertion and deletion. It is described in the paper: Pang, A., A. Smith., P. Nuin, and E. R. M. Tillier. 2005. SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution BMC Bioinformatics 6: 236. It is available as C source code and Windows executables. It can be downloaded from its web site at http://www.uhnresearch.ca/labs/tillier/software.htm

Cory Strope, S. D. Scott and Etsuko Moriyama of the Department of Computer Science and School of Biological Sciences of the University of Nebraska (cstrope (at) cse.unl.edu) have released indel-Seq-Gen version 1.0, a sequence family simulator incorporating domains, motifs, and indels. it simulates a more realistic evolutionary process of protein sequences including insertions and deletions (indels). iSG allows the user to simulate multiple subsequences according to different evolutionary parameters, which is necessary for generating realistic protein families with multiple domains. It tracks all evolutionary events including indels and outputs the "true" multiple alignment of the simulated sequences. iSG can also generate a larger sequence space by allowing the use of multiple related root sequences. It is intended to be used to test the accuracy of multiple alignment methods, phylogenetic methods, evolutionary hypotheses, ancestral protein reconstruction methods, and protein family classification methods. It is described in the paper: Strope, C. L., S. D. Scott, and E. N. Moriyama. 2007. indel-Seq-Gen: A new protein family simulator incorporating domains, motifs, and indels. Molecular Biology and Evolution 24: 640-649. It is available as C source code, Perl script, Linux executables and Intel Mac OS X executables. It can be downloaded from its web site at http://bioinfolab.unl.edu/~cstrope/iSG

  Dmitry Filatov, of the Department of Plant Sciences of the University of Oxford, U.K. (dmitry.filatov  (at) plants.ox.ac.uk) has released ProSeq (PROcessor of SEQuences) version 2.9. ProSeq is a sequence-editing environment that can do sequence alignment editing, translation, detection of polymorphic sites, and a variety of tests, many of a population-genetic nature, for neutrality and recombination. The part of its capabilities that are relevant to this listing is that it can simulate the evolution of a set of DNA sequences along a coalescent tree, with or without recombination. It is described in a paper: Filatov, D.A. 2002. ProSeq: A software for preparation and evolutionary analysis of DNA sequence data sets. Molecular Ecology Notes 2: 621-624. ProSeq is a Windows program available from its web site at http://dps.plants.ox.ac.uk/sequencing/proseq.htm.

  Paul Michael Agapow (p.agapow (at) ic.ac.uk), of the Department of Biology, Imperial College, Silwood Park, U.K. has released MESA (MacroEvolutionary analysis and SimulAtion), version 1.9.23, a program to simulate evolution of a group, allowing for a variety of kinds of extinction mechanisms. It can simulate evolution and describe the diversity of the resulting groups. MESA is available as an executable for Windows and as an executable for Mac OS X from its web site at http://www.agapow.net/software/mesa

Reed Cartwright of the Bioinformatics Research Center at North Carolina State University, Raleigh, North Carolina (racartwr (at) ncsu.edu) has written DAWG (DNA Assembly With Gaps), version 1.1, a program to simulate evolution of DNA sequences with recombination and gaps. It is designed to simulate the evolution of recombinant DNA sequences in continuous time based on the general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation. It accepts phylogenies in Newick format and can return the sequence of any node, allowing for the exact evolutionary history to be recorded at the discretion of users. Dawg records the gap history of every lineage to produce the true alignment in the output. Many options are available to allow users to customize their simulations and results. It is described in the paper: Cartwright, R. 2005. DNA Assembly with gaps (DAWG): simulating sequence evolution. Bioinformatics 21 (Supplement 3): iii31-iii38. It is available as C source code. It can be downloaded from its web site at http://scit.us/projects/dawg/wiki

Barry Hall of the Bellingham Research Institute in Bellingham, Washington (barryhall (at) zeninternet.com) has written EvolveAGene3, a program that simulates evolution of a protein sequence along a tree. It generates a bifurcating tree, and assigns branch lengths from a distribution whose mean is specified by the user. A protein sequence is evolved along this tree, with deletions and insertions of codons and with base subtitutions. Substitutions that change the amino acid are accepted with a specified probability. This includes having variable regions of selection intensity, positive or purifying, within the sequence and variation in intensity of selection over branches. Output includes the true tree and unaligned coding sequences and protein sequences as well as the true DNA and the true protein alignments. It is available as Perl script, Windows executables and Mac OS X universal executables. See the web site http://homepage.mac.com/barryghall/Software.html

   Robert Beiko and Robert Charlebois of the Faculty of Computer Science at Dalhousie University (beiko (at) cs.dal.ca) have released EvolSimulator version 2.10, a program to simulate the evolution of genes and genomes. EvolSimulator was created to allow the simulation of complex evolutionary regimes, potentially comprising nonstationary and nonuniform processes at the sequence level, alongside genome-level processes such as gene duplication, gene loss, and lateral gene transfer. Several models of LGT are implemented, including random transfers, transfers that favour close relatives in the organismal tree, and preferential transfer among members of the same habitat. It is described in the paper: Beiko, R. G. and R. L. Charlebois. 2007. A simulation test bed for hypotheses of genome evolution. Bioinformatics 23 (7): 825-31. It is available as C++ source code. It can be downloaded from its web site at http://bioinformatics.org.au/evolsim

Martin Senger (senger  (at) ebi.ac.uk) of the European Bioinformatics Institute, Hinxton, U.K. and Peter Ernst (P.Ernst  (at) dkfz-heidelberg.de) of the Deutsches Krebsforschungszentrum, Heidelberg, Germany distribute W2H, version 4.1.1, a web interface for running molecular sequence analysis programs. It can invoke a variety of sequence analysis programs, including the EMBOSS Embassy versions of a number of PHYLIP 3.5 programs. W2H is a set of web pages that has been developed primarily with Unix platforms in mind. They are available from the W2H web page at http://www.w2h.dkfz-heidelberg.de/.

  Juan José de Haro (jjdeharo (at) terra.es) of "una pequeña ciudad" of the province of Barcelona, Spain, has released Phyledit version 2.0. This is an interactive data editing and analysis program that uses PHYLIP and Treeview for analysis and display of trees. It uses eight programs from PHYLIP, all concerned with discrete 0/1 characters. Phyledit's menus, responses and documentation are all in Spanish. It is a Windows executable downloadable available from its web site at http://www.terra.es/personal7/jjdeharo/phyledit/. It is available there either by itself or with the PHYLIP and TREEVIEW executables as well.

  Øyvind Hammer, of the Paleontological Museum of the University of Oslo, Norway (ohammer  (at) nhm.uio.no) has written PAST (PAleontological STatistics), version 1.31, a package which carries out many kinds of paleontological data analyses, including stratigraphic and morphometric statistics. It also does parsimony analysis, including exhaustive, branch-and-bound and heuristic algorithms for Wagner, Fitch and Dollo parsimony. It does bootstrap methods, strict and majority rule consensus trees, and consistency and retention indices. It calculates three stratigraphic congruency indices with permutation tests. PAST is described in a paper: Hammer, Ø., D.A.T. Harper, and P. D. Ryan. 2001. PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4:, issue 1: http://palaeo-electronica.org/2001_1/past/issue1_01.htm. PAST is available from its web site at http://folk.uio.no/ohammer/past/index.html as a Windows executable. Manuals can be read online or downloaded from the web site.

Matthew Wills of the Department of Biology at the the University of Bath,. U.K. (bssmaw (at) bath.ac.uk) has produced GHOSTS version 2.4, a program for significance tests for RCI, SCI and GER values by randomization. It calculates the Relative Completeness Index (RCI), the Stratigraphic Consistency Index (SCI), and the Gap Excess Ratio (GER) measures of consistency of phylogenies with the stratigraphic record if given one or more tree topologies and stratigraphic range data for up to 74 terminal taxa. It can be used with NEXUS tree files and can be used interactively with MacClade. It can also randomly permute the assignment of stratigraphic ranges among taxa, while holding tree topologies constant, to yield a distribution of values. It tests whether the RCI and SCI values for the original data differ significantly from the random distributions. Its methods are described in the paper: Wills, M. A. 1999. Congruence between phylogeny and stratigraphy: randomization tests. Systematic Biology 48 559-580. It is available as source code for use with Chipmunk Basic. It can be downloaded from its web site at http://palaeo.gly.bris.ac.uk/cladestrat/Gho2.html

Andrew Rambaut (andrew.rambaut  (at) zoo.ox.ac.uk) of the Department of Zoology, University of Oxford, has released QDate version 1.1.1. QDate estimates the date of divergence between two pairs of sequences given that the date of divergence of the members of each pairs is known. It analyzes the data under three models: (1) a perfectly clocklike model, (2) a model in which one pair has a different rate of divergence than the other, and (3) a model in which all branches have different rates. The method is described in the paper: Rambaut, A., and L. Bromham. 1998. Estimating divergence dates from molecular sequences. Molecular Biology and Evolution 15: 442-448. QDate is available from its web site at http://evolve.zoo.ox.ac.uk/software.html?id=qdate. It is available as C source code for Unix or as a Macintosh or Windows executable.

Andrew Rambaut, of the Department of Zoology, University of Oxford (andrew.rambaut  (at) zoo.ox.ac.uk) has written TipDate version 1.2. TipDate is an application for estimating the rate molecular evolution (and hence a time-scale) for a phylogeny consisting of dated tips. These will most frequently be from viruses or other fast-evolving pathogens that have been isolated over a range of dates. The program can also return the likelihood for the simple molecular clock model (i.e., assuming that all sequences are contemporary), for a model in which rates of change at different times are drawn from a distribution, or the non-clock model. These are useful for likelihood ratio tests of the fit of the model to the data. TopDate is described in a paper: Rambaut, A. 2000. Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics 16: 395-399. TipDate is available as Mac OS executables and as source code for Linux or Unix from its web site at http://evolve.zoo.ox.ac.uk/software.html?name=TipDate. It is also available in a web-based server version from the Pasteur Institute server.

Emanuel Paradis (paradis (at) isem.univ-montp2.fr), of the Institut des Sciences de l'Évolution of the Université Montpellier II and the CNRS, Montpellier, France has released Diversi version 0.20.0, a program for the analysis of diversification using phylogenetic data. It uses several methods to estimate and test for variations in diversification rates using phylogenetic data, including tests for temporal or among-clade variations in diversification rates using a maximum likelihood method. The program takes divergence times as its input. It can also simulate the branching of trees. he tests are described in a paper: Paradis, E. 1997. Assessing temporal variations in diversification rates from phylogenies: estimation and hypothesis testing. Proceedings of the Royal Society of London B 264: 1141-1147. It is available as FORTRAN source code and also as a Windows executable, from Paradis's software web page at http://www.isem.univ-montp2.fr/PPP/PPPphylogenie/ParadisHome.php#softwares or by ftp from evol.isem.univ-montp2.fr in directory /pub/pc/Log-manu. Paradis describes DIVERSI as no longer developed or maintained, and soon to be superseded by his later program APE.

Marc Robinson-Rechavi, of the Laboratoire de Biologie Moléculaire et Cellulaire of the École Normale Supérieure de Lyon, France (marc.robinson  (at) ens-lyon.fr) has written RRTree, (Relative Rate tests within a Tree), version 1.1. It carries out relative rate tests for equality of evolutionary rates in DNA or protein sequences between lineages, taking into account the structure of the tree, which can be input in a number of common formats. In addition sequences are read in. The methods are described in a papers:

• Robinson, M., M. Gouy, C. Gautier, and D. Mouchiroud. 1998. Sensitivity of the relative-rate test to taxonomic sampling, Molecular Biology and Evolution 15: 1091-1098.
• Robinson-Rechavi, M. and D. Huchon. .2000. RRTree: Relative-rate tests between groups of sequences on a phylogenetic tree. Bioinformatics 16: 296-297.