Bugs in PHYLIP, known or recently fixed
The hemipteran Thasus, a true bug
This page shows only recent bugs, but we make this listing cumulative so that
it will have ever more material on it (we never run out of bugs). Not all
bugs we find or fix can be shown -- these are only the most dramatic ones.
Known bugs (we're working on them)
Bugs we know how to fix; the fixes will appear in the next release
- At a number of points in the main documentation file for version 3.695,
the version number of the package is described as 3.7a, or the folder in
which the package is to exist is named phylip-3.7a. These of
course should have been respectively 3.695 and phylip-3.6. There
actually will be no version 3.7; the next major release will be version 4.0.
- People trying the compile the source code in Linux or other versions of
Unix cannot simple type the command make install while the current
folder is the src folder. That would require a makefile named
Makefile . But in version 3.695 the Linux/Unix makefile is actually
named Makefile.unx . It is probably as simple as
going into the src directory, copying
calling the copy Makefile , and then typing the command
which will cause the programs to be compiled and the executables and font
files installed in the exe directory. Alternatively, you can type the command
make -f Makefile.unx install
- Dnadist has an error for the case in which sites are weighted (menu option
W). In those cases some subscripts of an array are generated which cause
memory access violations (elements before the start of the array are accessed).
If you can recompile the program, the problem can be fixed by adding one line
to the code. Just before line 642, add the line
if (location[ally[i]-1] > 0)
so that the code there now reads:
for (i = 0; i < sites; i++)
if (location[ally[i]-1] > 0)
weight[location[ally[i] - 1] - 1] += oldweight[i];
Bugs we are still intending to work on and haven't yet fixed
- In Mac OS X 10.9 (Mountain Lion) there is a file execution permission
problem: Mountain Lion will not run executables of PHYLIP programs when
you click in their icons. It complains that the developer name is unknown. This
is a security feature. There is an easy workaround for this that needs to be
done once for each program. If this occurs, try control-clicking on the program
icon instead. Select Open. When you are then asked whether you want to open
this program, select Open. The program will open. This
allows the program to
be opened in the future simply by clicking on
the executable icon. So it only needs to
be done once for each of the programs in PHYLIP, and after that the program can
be run by clicking on the icon for that program. We hope to avoid this in
future versions by signing the programs with my Apple Developer identity. As
far as I know, this problem does not arise if you open a program in a Terminal
window by typing its name.
- Fitch has a bug (or lack-of-feature). When an input tree has a
multifurcation (other than a trifurcation at its base) then Fitch uses only
the first two "furcs" at that fork. The result is that the tree it
reads in lacks some species, and of course that can cause further problems.
This will often be a problem for people who are using a consensus tree
from boostrapping and want to use Fitch to infer branch lengths for it.
The best we can suggest is that you either (1) use Dnaml or Proml together
with the original sequence data and the input tree -- Dnaml will correctly
read your multifurcating input tree, or (2) use Retree to take each
by hand, resolve it into a series of bifurcations by removing and re-adding
lineages and making the new branches have lengths zero, and then once the tree
is bifurcating, use it as an input tree with Fitch.
- Promlk seems not to be functioning properly. (Fortunately, Promlk is
one of the less-used programs in the package). When it searches for the
best tree it seems to get a tree with all branch lengths of zero, which is
blatantly wrong. When it is used in U (user tree) mode with an input
tree file, but re-estimating the branch lengths, it also gets zero branch
lenghts. Only when it uses the U (user tree) mode, not re-estimating
the branch lengths, but using the ones in the user-defined tree, does it
work properly. These problems seem to have been present since version 3.69.
Be cautious about any runs with this program.
- When Fitch is used on only three species, it results in blank output.
We need to put in an error message about this. People needing to do a
distance matrix tree on three species should use Neighbor instead. Of
course, for three species there is only one possible unrooted tree, and
that's what you get, with the sums of the branch lengths between each
pair of species adding up exactly to the observed distances.
- When Seqboot is used on discrete morphological (0/1) data, and
one uses the Factors feature while choosing the option of
permuting the order of characters, invalid (null) characters are
produced in the output file, and the output is presumably invalid.
It may take some time to untangle this one.
- On Mac OS X, Retree crashes if you construct a tree yourself but make it
only 2 species.
- On Mac OS X, when Drawtree is asked to show in the preview a label which has a non-Hershey font at an
angle in a preview, it instead shows it horizontally. The final plot is OK,
- On Mac OS X, when Drawgram is asked to show in the preview a label which
has a non-Hershey font at an angle, it shows it as a Hershey font instead,
and the spacing of the labels is then wrong, both there and in the final
- On Mac OS X, running the 32-bit executables that we distribute,
there can be memory problems with Proml for large data sets. In particular,
Proml allocates some more memory for each data set run, so in a
multiple-data-set run such as a bootstrap run, with enough replicates one can
exceed the 4 GB of memory that is all that can be addressed with
32-bit code. We think that this problem does not affect the results, as
it is most likely just failure to deallocate the memory before allocating
again. Here are two possible solutions:
- Recompile Proml in such a way that
64-bit code can be created, which would enable Proml to use all the
available system memory.
- Another is to take the bootstrap replicates, divide them into
separate files, each with (say) 1/5 of the replicates. Run Proml on each
separately, and then take the resulting tree files and
concatenate them into one bigger tree file before running Consense.
These are listed by the version of the package that fixed them, in reverse
chronological order (i.e., latest first). To see what bugs you have in
the version of PHYLIP that you have, read down, stopping when you reach
- version 3.697 (December, 2017)
The bug recently found in the consensus-tree code by Makoto Shimada and
Tsunetoshi Nishida, and described in their paper in Molecular Phylogenetics
and Evolution (volume 109, pages 409-414, 2017) is now fixed using the fix
that they provided. This is for the source code. The executables are
currently still at version 3.695, and so still have this bug. The bug makes
no difference if the product of the number of species times the number of
trees is less than 32767, as it only has an effect when the hash table of
partitions found overflows, and has to be expanded and repopulated.
- version 3.695 (April, 2013)
- Thanks to Brian Fristensky for pointing out that the L option (restriction
site length) in the menu of Restml does not work. When you select it, nothing
happens. This is because of a simple error in line 930 of restml.c
where the letter L got left out of the string. But there is an easy workaround
without recompiling Restml. Just (1) select the U option (user-defined tree),
(2) now the L option can be selected and you can change the restriction site
length, and (3) if you're not going to use a user-defined tree, then just
select U again. You'll be back to searching for the best tree and the
restriction site length will have been changed.
- We have received a number of reports that Drawgram and Drawtree will not
run on some (all?) Mac OS X 10.6 (Snow Leopard) systems. Instead an error
message appears saying that the Classic environment is not available (which is
weird since Classic was for Mac OS 9 code, which this is not). An alternative
A full fix for this problem will be difficult. We have been aware for some
time that Mac OS X has ceased support for the Carbon windowing system and
wants us to instead use the more recent Cocoa system, and the Objective C
programming language. This will require some serious programming, and we
do not currently have a programmer to do it. If any of you want to try, you
should contact me.
- Go into the src folder in the PHYLIP folder and recompile
Drawgram and Drawtree by issuing the commands make drawgram and
make drawtree. This will cause the GCC compiler to compile
versions of Drawgram and Drawtree that do not use the Mac OS X Aqua windowing
system but use X Windows instead.
- These two executables can then be
moved to the exe folder.
- They can be run by activating the X Windows system. The
X Windows icon will be found in the Utilities folder which is in the
Applications folder (use the Finder window).
- Once the X11 terminal window appears (if it does not appear it can be
activated by using the Applications menu of the X11 application), navigate to
the exe folder using commands such as cd
- The program can then be run by typing the command ./drawgram or
- Treedist is using too much memory, which makes cases with large
numbers of species and large numbers of trees unable to run.
If you can recompile, the following fix should help:
These will reduce the memory useage while allowing the program to
still calculate the distances.
- In cons.c, add a line after line 1382:
*timesseen[i] = 0;
- In treedist.c, add a line after line 1206:
maxgrp = 4*tip_count;
- version 3.69 (September, 2009)
- version 3.68 (August, 2008)
- version 3.67 (July, 2007)
- We had our first reports on the behavior of PHYLIP Windows executables
on Windows Vista. The programs work fine. The only thing that did not
work is the self-extraction program that unpacks the archives. For some
reason it did not work on Vista. The work-around was that, after you got
an archive file like phylipwx.exe onto your system, you had to change the
from "exe" to "zip". Then you had to click on the file. You were presented
with options including "Extract all files". If you chose that the archive
was unpacked. The programs would then work. Although we provided "zip" archive
versions of the package, we have now got a new version of WinZip which is
supposed to have a self-extractor that works on Windows Vista, and it was
used to produce the self-extracting archive since 27 August 2007.
- On Mac OS X systems, if our distributed executables are placed in
a folder whose path contains a name with an internal blank, such as
/Users/ianr/the files/ then the script that causes each of our
programs to run when you click on the corresponding icon does not work, and
there is an error message. This is a scripting error in our Mac OS X setup,
and it was corrected in version 3.67. In the meantime, if you have this
problem, the solution is to put PHYLIP in a folder whose path does not have any
folder that has a blank in its name. In the above example, all that would be
necessary is to rename the folder the files to the_files
- We are still getting reports of stickiness of the tree, and occasionally
of negative branch lengths, in Dnamlk and Promlk which do not do as good a job
of searching for best trees as they should. This has turned out to be an
issue of nodes getting stuck when they collide in moving them on the "time"
scale. Some major changes were in the code in the 3.67 release to
eliminate this stickiness and give a good search.
- An error was made in putting together the matrices for the PAM
mutation model in Protdist, Proml, and Promlk. These programs will
give PAM calculations inconsistent with earlier (v3.65 and before)
versions, and with other programs. The matrices were corrected
in version 3.67. This does not affect JTT or PMB models.
- The W (within-species varation) option of CONTRAST uses somewhat incorrect
equations to infer within-species covariances and phylogenetic covariances.
These were corrected in version 3.67. Anyone severely impacted by the
problem in the meantime should contact me.
- Protdist sometimes results in distances greater than or equal to 100.000.
When this happens, the distance can run together with the previous number in
the output file. For example, a distance of 0.31766 followed by one which is
127.43986 might look like this: "0.31766127.43986". This causes trouble in
any program that tries to use this distance matrix. One symptom of this
may be the program reporting that two distances which are expected to be
equal are unequal -- but then printing them both out, and they appear to be
equal! In this case it would print out a message warning you that
0.31766 was not equal to 0.31766. It is doing so because one of them is
actually seen by it as 0.31766127 and the other 0.31766. In all future
versions, there will be a blank printed between the two numbers. For the
present, use an editor to find them and insert the blank by hand. If this
is difficult, a Sed script (which can be used on Linux or Unix machines)
has been written by Doug Scofield, and is available from him at:
Many thanks to him for this. As you can see, this problem is the result
of us not thinking of what happens when the distances are big, and the
fix in the code is trivial -- just ensuring that there is at least one
blank between successive distances.
- Contml, with gene frequencies, has a bug in the transformation to
variables that have approximate Brownian motion as their evolutionary
process. This can lead to wierd trees. It might be preferable to go back
to the 3.5c version if you need to use Contml for this. We believe that
this will be correctly fixed in the 3.67 version. If people can recompile
the source code, they replace the function transformgfs with
this one and recompile (you should be able
to save it from your browser using the Save As choice in its
- version 3.66 (August, 2006)
- Program Treedist was found to compute the Branch Score Distance
incorrectly. It will, in most cases, get the branch lengths in
terminal branches incorrect and then be likely to find a nonzero distance
between trees when they are really identical, and incorrect distances
when they are not identical. Alas, there is no workaround to avoid this.
All distances done with this option before version 3.66 should be regarded as
unless all terminal branches have the same length, or unless the order
of species in the tree is the same as in the first tree in the file.
The Symmetric Difference option, which does not use branch lengths,
- Program Dnamlk, when run on Linux or Windows systems, sometimes gave
negative branch lengths for some branches on the tree. This is bad.
Although we at first thought that this was a compiler bug, it seems to
be a lack of initialization of some pointers. Program Promlk may have
the same problem, as they share code.
If you have this problem you can work around it by
not using the Global menu option when running Dnamlk (or Promlk). If you
extensive tree search the J (Jumble) option may be your best bet.
- On Windows (at least, on Windows xp), our executables for version 3.65
produce output files (outfile) and output tree files
(outtree) that have end-of-line characters that result in their
being hard to read on the Notepad editor. They appear as one big line. If you
use the Wordpad editor, or Microsoft Word itself, the files will be readable.
This is and end-of-line compiler setting we got wrong when compiling the
- Programs Dnaml and Proml sometimes failed to iterate branch lengths in
trees enough -- this can result in them failing to find as good a tree as
the molecular clock versions Dnamlk and Promlk, a phenomenon that is not
supposed to occur. The problem results from the iteration code in
function makenewv giving up too easily when branch lengths are
very short. The resulting branches get "stuck" at length 0 when they
should not. If you can recompile the programs, the problem can be solved by
the following changes:
We think these fix the problem. Some more thorough fixes are implemented in
the 3.66 code.
- In file phylip.h change the value of the constant iterations to 8 instead of 4.
- In files dnaml.c and proml.c, change function
makenewv to replace
done = fabs(y-yold) < epsilon;
done = fabs(y-yold) < 0.1*epsilon;
- In dnaml.c, in function makenewv, also replace*
if (yold < epsilon)
yold = epsilon;
if (y < epsilon)
y = epsilon;
- The Mac OS X archives (in .dmg form) appeared at first sight not to have
any executables directory in the package. This is owing to strange placement
of icons once we package the files. The
OS X executables are there -- their folder is just way down the
window. Use the scroll bar to look for them.
You should be able to use the View/Rearrange menus to
make the folder icons appear in a more reasonable place. (Or this can be
done once all of the contents of the .dmg archive are copied out to another
- Programs Dnaml and Proml (but not Dnamlk or Promlk), from version 3.64
on, crashed if the Categories (C) option is used, even if all categories are
the same rate of change. This unpleasant behavior does not occur if the
menu option for "Speedier but rougher analysis" is changed to "No, not rough".
That slows down the run but allows it to succeed.
The fix turns out to
be that all instances in dnaml.c of calls to function copynode
(or all instances in proml.c of calls to prot_copynode) that
involve an argument lrsaves should have the third argument be
rcategs instead of categs.
- In Seqboot, when menu item J is set to Permute species within characters it is impossible to change menu item W (character weights). This is
a glitch in the menuing code. If you can change the source code and recompile,
change at line 215 of seqboot.c:
((permute || ild || lockhart)
&& (strchr("ACDEFSJPRXNI%1.20",ch) != NULL)) ||
(permute && (strchr("ACDEFSJPRWXNI%1.20",ch) != NULL)) ||
((ild || lockhart) && (strchr("ACDEFSJPRXNI%1.20",ch) != NULL)) ||
If you are stuck with our executables and need this feature, you can also
work around it in the following devious way:
- Set menu item J to some other setting where menu item W appears in the menu,
such as Bootstrap,
- Change menu item W
- Then change item J to Permute species within characters
- Our Makefile for Unix had some problem finding some of the
X-windows libraries on Mac OS X systems on Intel Macs. This prevented
the compilation of Drawtree and Drawgram. You might have had to use
those two programs by using their PowerMac Mac OS X executables.
All the other programs did compile and run correctly on Intel Macs.
- version 3.65 (August, 2005)
- version 3.64 (July, 2005)
- Treedist had trouble on Windows systems
reading trees. This was due to problems with the ftell command on
CygWin. It has been fixed by having the files read as binary files.
- Trees with branch lengths compared using Treedist may have
incorrect distances when evaluated as unrooted trees, owing to
miscalculation of branch lengths for the bottommost branches.
- Runs of Seqboot on Mac OS X systems with gene frequencies data have
showed incorrect results -- wrong numbers of loci sampled, for example.
This is due to bad code generated by the Metrowerks Codewarrior compiler
when set to higher levels of optimization (our source code is OK). We
will recompile the program at a lower level of optimization in the next
bug-fixing release. If you can follow our compiling instructions and have
this compiler, you can produce a correctly working executable. Alternatively
you can use the gcc compiler and use our Unix Makefile to recompile this
program (by typing "make seqboot"). This is quite easy to do and all Mac OS X releases have the
gcc compiler in them -- it only needs to be installed.
- In runs of Proml, Dnaml or Restml with user trees, if one puts in a user
tree with an internal multifurcation and asks the program to re-estimate
the branch lengths for that tree, the branch lengths in only two of the
furcs will be re-estimated if they already have branch lengths.
This is due to a bug in the function "initrav"
causing it to fail to enter one or more of the subtrees. A workaround until
the next release is as follows: Use Retree to remove all branch lengths
on the tree. The tree's branch lengths will then all be re-estimated
when it is used as a user tree.
- The example output in the Treedist documentation gives distances
computed by version 3.62 or earlier, in which the tree distance is not
- version 3.63 (December, 2004)
- The DNA and protein likelihood programs could have problems with
underflow if very large numbers of sequences were analyzed. Underflow
protection code was needed to make this much less likely to happen.
- A number of programs had the problem that when M (multiple
data set) runs are done, if the data sets differ in the number of
characters from data set to data set, they only allocate enough memory for
the first data set, and then can crash on subsequent, larger, data sets.
For bootstrap and permutation runs this should not be a problem, but
for jackknife runs it might be. One work-around until we fixed this was to
move the data set with the most characters to the front, so that enough
space is allocated. The programs we think had this problem are:
Clique, Dnacomp, Proml, Promlk, Protdist, Dollop, Gendist, Pars, Restml, and
- When the Branch Score distances are computed in program Treedist, the
sum of squares of differences between branches was not square-rooted, as the
documentation web page says it is.
- Fitch and Contml may die when asked to do Jumbling, in some cases.
- Dnaml had inconsistencies in results when branch lengths of a user tree
were estimated, and when the same numbers were provided in the user tree.
- Trees fed into Contrast could cause trouble if they contained unifurcations
(forks with only one descendant). The program did not complain about this, as
it should have.
- End-of-line characters in input files
in certain cases caused trouble in Mac OS X (for example when the files came
over from Windows).
- When printing a rooted tree out in Kitsch, the root was not placed
intermediate between its two decsendants.
- The variable numtrees was sometimes used when still uninitialized
- Restdist had a site-aliasing bookkeeping bug that could lead to incorrect
- Restml would not allow site lengths greater than 8, because an array
was of fixed size when it should have been dynamically allocated.
- The variable name howmany conflicts with predefined names in
some older Sun compilers. It will henceforth be deliberately misspelled to
- With larger data sets being analyzed, Proml, Promlk, Dnaml, and Dnamlk
have had to have underflow protection code installed, as likelihoods were
getting too small.
- Treedist was giving wrong answers when asked to compute all distances
between trees in two files that had unequal numbers of trees. This was a
- The variable scanned was uninitialized in the Drawtree and
Drawgram programs, which could sometimes cause problems.
- The lack of initialization of a variable, delta in Dnadist
meant that different results could be obtained from interactive runs than
were obtained in runs under the control of a command file.
- Dnadist was sometimes stopping when encountering sequences that had an
infinite or indeterminate distance (i.e. when the sequences were too different
or when they had no sites in common), when it should have printed out "-1"
and continued. When it was supposed to print "-1" in some recent versions
of PHYLIP it printed "1.0000" instead.
- version 3.62 (September, 2004)
- The ftp link used by our "Get Me PHYLIP" page to fetch the version 3.62
Linux gzip'ed sources and documentation archive was incorrect until recently (I
hadn't updated it to fetch version 3.62). If you had trouble fetching
this archive in version 3.62, please try one more time. It will work now.
- A number of people have found, with Fitch and with Contml, that version
3.61 crashes on multiple Jumbling (option J) or on bootstrap runs. This is
fairly serious. It does not happen with versions of these programs earlier
than 3.6 (such as 3.6a3 or 3.573c). This release fixes these problems.
- version 3.61 (August, 2004)
- In dnaml.c there was some mistaken code doing rate
standardization that made the program compute incorrect likelihoods
for user-defined trees where the program is using their branch lengths.
- In dnaml.c some bookkeeping code associated with tree
structures caused it to crash after only a few replicates when you
do a multiple data sets run (for bootstrapping).
- The code for the Shimodaira-Hasegawa test has been in error for some
time. The effect of this will be to cause the test to fail to find
significance in some cases where it should. This affects Shimodaira-Hasegawa
tests (ones with more than two user trees) for many of the programs.
If you have downloaded
version 3.6, I urge you to replace it with 3.61 as soon as you can. If you
have done SH (Shimodaira-Hasegawa) tests, I recommend strongly that you
rerun those using version 3.61.
- version 3.6 (July, 2004)
- The transform of gene frequencies to Brownian motion in Contml was not
very good. It has been replaced by an extension of the 1975 method in
Elizabeth Thompson's book Human Evolutionary Trees, using orthogonal
coordinates on a plane tangent to the mean of the gene frequencies among species.
- In Retree, when you delete two adjacent clades, the stem connecting
them wasn't marked on the screen as deleted.
- Numbers in the Contrast output could run into each other if too big.
- There was no error message for negative branch lengths in Contrast.
- Dnadist was blowing up if two sequences are identical for some distances.
- Gendist sometimes made 0.00001 diagonal elements in the distance matrix.
- Consense generated segmentation-faults on larger cases with more than 1,000 trees.
- Dnamlk and Promlk could get wrong likelihoods and wrong reconstructions
of ancestral states, when there were all of these: gamma-distributed or HMM
rates, some autocorrelation among sites, and some sites with weight 0.
- version 3.6b (July, 2003)
- Dnadist versions 3.6a2 and 3.6a3 have a bug that makes it calculate zero
values for the similarity between two sequences when the table of fractions of
similarity between two sequences is being computed, and when one or both of the
sequences has a nucleotide that is ambiguous other then "N", "?", or "-". It
affects only similarity values, not any of the distances that Dnadist can
compute. To calculate similarity values for those sequences, make a version of
your sequence input file that omits those sites. This is necessary only for
those sequences -- for all other purposes you should use the values from the
- Proml has a bug that apparently prevents it (in User tree mode) from
re-estimating the branch lengths of a tree. This means that if you take a
consensus tree and try to re-estimate its branch lengths, it will instead
leave them with the branch lengths that Consense gave them. In the meantime,
there is no workaround to let you infer branch lengths with the U option, alas.
- When distances between trees in a file are computed by Treedist, the
Windows executables have a segmentation fault on the case where we do distances
among all pairs of trees in one file. Users can work around this by
duplicating the file and computing instead all distances between trees in one
file and trees in the other, which somehow works.
- Treedist does not give sensible results when the trees in an input
tree file do not all have the same list of species. We only intended
Treedist to be used with the same list of species in all trees, but there
is no error message preventing data of this sort from being analyzed at
- On G3 or G4 Powermacs with MacOS 9.2.1 or earlier, the PHYLIP 3.6a2.1 and
3.6a3 executables for most programs sometimes fail to allow you to give them
valid output file names, complaining that they are invalid (when they aren't). This is
presumably some interaction between our Metrowerks Codewarrior compiler
and those versions of MacOS. If you have this problem you can fix it
either by upgrading to MacOS 9.2.2 or by running MacOS 9 under MacOS X.
We would be interested in hearing which versions of MacOS our code
works in, and with which processors.
- When two adjacent branches on a tree have zero length, and one plots
the tree using Drawtree, the labels are sometimes superimposed on each other
and also plotted in the wrong place. A temporary fix until we correct this is
to make the branches have nonzero but tiny lengths such as 0.00001.
- When you use a data set with three species on some of the programs,
it will not process them properly because the algorithm assumes that
there are at least 4 species.
- version 3.6a3.1
A revised version of the Mac executables and sources corrected some bugs
that were causing trouble only on that platform:
We have not yet upgraded the non-Mac sources and executables as these
problems were Mac-specific.
- Treedist would not open an output file.
- Lines in the Macintosh previewing for Drawgram and Drawtree were
sometimes too thin to be visible.
- Drawgram and Drawtree had their default memory size set larger as Drawgram
would usually refuse to run.
- Error messages for being unable to open an output file repeated the
word "file" unnecessarily.
- Pars had the wrong icon, owing to an obscure resource problem.
- version 3.6a3 (July, 2002)
- version 3.6a2.1
- A quick correction of 3.6a2 since:
- The coefficients of variation of rates among sites (and
therefore the alpha shape parameter of the Gamma distribution
were set incorrectly after being input by the user.
- The documentation said Old Style programs read their
user-defined trees read from file infile -- this was
corrected in the documentation to say file intree.
- version 3.6a2 (July, 2001)
- These bugs which were present in version 3.6a were corrected
- Kitsch: couldn't process user trees.
- Dnacomp, Dnamove, Move, Dolmove, Dollop: couldn't read
User with branch lengths successfully
- Dnamlk: was a tendency for nodes to get stuck together.
- In Treedist identical trees had nonzero distances if the
names of the species were numbers.
- Dnadist: there was a problem with data sets that had a space
after last nucleotide of a segment of sequence.
- Some of the programs had trouble with jackknife-sampled
data sets (produced by Seqboot) which had different numbers of
sites (characters) in different replicates.
- Some of the sequence programs had data-reading problems
when there were blanks before a segment of sequences in the
interleaved data format.
- version 3.6a (July, 2000)
- This "alpha release of 3.6 fixed some bugs that had been encountered
over the years since version 3.573. Here are some of them:
- PROTDIST read in weights but did not use them. To get
it to use them one can replace the code in line 1446 of protdist.c
lnlike += weight[k]*log(p);
slope += weight[k]*dp / p;
curv += weight[k]*(d2p / p - dp * dp / (p * p));
- The output file generated by PROTDIST contained a section at
its front that gives a table of the weights. This would prevent it from working
as an input file in the distance matrix program. If this section
is edited out, the distance matrix programs will read it properly.
- The 3.573c Windows95/98/NT executables had trouble
running DRAWTREE and DRAWGRAM on many systems. If you see an
error saying: DOS/4GW fatal error (1004): syntax is DOS4GW <executable.xxx> you should try various placements for DOS4GW.EXE.
If none works you can use an MSDOS window to execute the command
- When you put a data set that has one or more nucleotides absent
(such as having no G's at all), DNAML and DNADIST's Maximum Likelihood
option could get upset and divide by zero. A temporary solution was to
use the F option to input four base frequencies, none of which are 0.
- If you used "outfile" as the input file name for most programs,
terrible things happened. The program opened "outfile" as a
file to put output into (thus erasing its contents) and then tried to
read its data from this empty file, causing a psychological crisis.
The solution is to rename "outfile" (to "infile" or almost anything
else) before using it as an input file for the next program.
The 3.6 fix of this problem is to warn the user when about to
write output that the file already was in use, and give the user
the opportunity to use a different file name.
- Retree and the user trees options of many programs choked on trees
that have comments like "[0.1000]" at the end of the tree, which is the way
some of our programs such as Dnapars have of indicating what
fraction that tree is of all trees generated by a run. If you want to
get versions before 3.6a to accept these trees, you
should remove these extra comments at the end of the trees and see
if this fixes it. However that error message is also the one you
get when you incorrectly try to use a rooted tree in a program that wants an
unrooted tree (see our Frequently Asked Questions ).
- If a data set that has two or more species that have the same name was
used to create a set of trees, and these were fed into Consense, one could get
groups appearing in the consensus trees that have more than 100% support, and
there is no error message about this.
This can be avoided by making all species names different before producing the
- When species names in the data had underscores in them (the "_" character)
and a tree file was used, the underscores in the tree file got translated into
blanks, and then the program would complain that it can't find that species
in the data. Changing the underscores in the species names of the data file to blanks or
changing the names in both files to dashes (or anything) will solve this.
- version 3.573
- There were multiple reports of PHYLIP programs not working on
MacOS 8.5. We cured this by recompiling it on an 8.5
system with a newer version of the Metrowerks compiler.
- Our PowerMac executables had been crashing if a row of dots was printed out
that reached the right-hand margin of the text window. Some programs
would do this on large data sets (unfortunately those windows are too
primitive to be resized). To cure this, you spreviously had to turn off the
option in the menu that instructed the program to report on the progress of the
run. In some cases this meant that you did not know when the run had
finished, except that then the File menu once again responded to the
mouse. This problem has now been cured by recompiling with a later version
of the Metrowerks compiler.
- Fixed memory allocation bug in Dnapars which caused it to crash on
long runs such as multiple bootstraps.
- Our Windows version has not been a good citizen when running on
Windows95 systems. It tended to hog the machine and not let other
programs and processes get enough processor time. This has been
a result of having only 16 bit (Windows 3.1) style Windows
executables. With this version we have now made
available 32 bit Windows executables as well. These work on
Windows95, Windows98, and WindowsNT, and they should allow other processes
and programs to proceed.
- version 3.572
- DnaMLK failed to correctly iterate branch lengths in some user tree
- SeqBoot generated bootstrap files of sequences that had the number of
sequences and the number of sites running into each other, with no
blank in between, when there were 10,000 sites of more.
- Our PCL (Hewlett-Packard Laserjet) drivers in Drawtree and Drawgram
generated code that will not print correctly on inkjet printers such as
the HP Deskjet series. This was apparently due to the version of the
PCL language that we assume being later than the version implemented in
- Mix printed out the wrong numbers of steps for user trees after the
first user tree. When it is asked to evaluate several users trees it
assigns them all the same number of steps, which is the number for the
first user tree.
- version 3.57
- The Windows executables were not able to run on Windows 95, so we
recompiled them with the Watcom C++ 10.5 compiler, and now they should
run well under either Windows 3.1 or Windows 95.
- Removed the flawed program Coallike (use our other package LAMARC instead).
- Memory allocation problems in Dnapars prevented some bootstrap runs from
- File ownership problems in PICT files produced by our executables of Drawgram
and Drawtree in the 680x0 Macintosh and PowerMacintosh versions.
- versions 3.56
- The input for the Categories option in various programs would not
read correctly in the Macintosh versions.
- The Categories and Weights options would not work together properly
in DnaML, DnaMLK, and Dnadist, which have both of these options.
- More species were allowed in Retree (500 instead of 100).
- PICT files output was being written incorrectly in Drawgram and Drawtree.
- New icons were drawn for the Macintosh executables. These icons were
also set up for the Windows executables.
- The BinHex (.hqx) file format was added to our ftp area as an alternative
method of distributing our 680x0 Macintosh executables.
- versions 3.54 and some executables of 3.55
- The PowerMac executables became available, thanks to Don Gilbert of
Indiana University, who first compiled them.
- Problems reading options in our Macintosh code.
- Incorrect algorithm for generating permutations in SeqBoot (thanks to
James Brown of AFRC in England for detecting this and suggesting the fix).
- Some problems with the DnaMLK categories (C) and jumble (J) options.
- Executables for 386 Windows and for 386 DOS were recompiled to allow
more adequate stack size.
- 386 Windows executables had math coprocessor emulation set up incorrectly
and would give strange results (fortunately, easily noticeable strange
results) on 386 or 486 systems that did not have math coprocessors (such
and 486sx processors). This was fixed by using the WEMU387.386 emulation
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