DNADIST. Computes four different distances between species from nucleic acid sequences. The distances can then be used in the distance matrix programs. (See the Distance Matrix programs pages for information on them). The distances are the Jukes-Cantor formula, one based on Kimura's 2- parameter method, the F84 model used in DNAML, and the LogDet distance. The distances can also be corrected for gamma-distributed and gamma-plus-invariant-sites-distributed rates of change in different sites. Rates of evolution can vary among sites either in a prespecified way, or according to a Hidden Markov model. The program can also make a table of percentage similarity among sequences.
PROTDIST. Computes a distance measure for protein sequences, using maximum likelihood estimates based on the Dayhoff PAM matrix, the JTT matrix model, the PBM model, Kimura's 1983 approximation to these, or a model based on the genetic code plus a constraint on changing to a different category of amino acid. The distances can also be corrected for gamma-distributed and gamma-plus-invariant-sites-distributed rates of change in different sites. Rates of evolution can vary among sites in a prespecified way, and also according to a Hidden Markov model. The program can also make a table of percentage similarity among sequences. The distances can then be used in the distance matrix programs.
GENDIST. Computes one of three different genetic distance formulas from gene frequency data. The formulas are Nei's genetic distance, the Cavalli- Sforza chord measure, and the genetic distance of Reynolds et. al. The former is appropriate for data in which new mutations occur in an infinite isoalleles neutral mutation model, the latter two for a model without mutation and with pure genetic drift. The distances are written to a file in a format appropriate for input to the distance matrix programs.
RESTDIST. Distances calculated from restriction sites data or restriction fragments data. The restriction sites option is the one to use to also make distances for RAPDs or AFLPs. The distances can then be used with the distance matrix programs
SEQBOOT. Reads in a data set, and produces multiple data sets from it by bootstrap resampling. Since most programs in the current version of the package allow processing of multiple data sets, this can be used together with the consensus tree program CONSENSE to do bootstrap (or delete-half-jackknife) analyses with most of the methods in this package. This program also allows the Archie/Faith technique of permutation of species within characters. It can also rewrite a data set to convert it from between the PHYLIP Interleaved and Sequential forms, and into a preliminary version of a new XML sequence alignment format which is under development and which is described in the SEQBOOT documentation web page.
FACTOR. Takes discrete multistate data with character state trees and produces the corresponding data set with two states (0 and 1). Written by Christopher Meacham. This program was formerly used to accomodate multistate characters in MIX, but this is less necessary now that PARS is available.