PAUP* Test Version Downloads
PAUP* test-version downloads
Status of PAUP*:
NOTE: Mac and Windows GUI versions have been updated to (unexpired) 4.0a139. Linux and command-line
versions are still underway.
PAUP* is undergoing rapid changes, and will soon be available as a quasi-commercial program
with a full GUI interface for both Macintosh OSX and Microsoft Windows (available from Sinauer
Associates), and a free, open-source command-line
version. While final development and testing is underway, we are making these test versions available
as a free download. They will expire every few months, and you will need to update when this happens.
Versions can updated using either an auto-updating system (GUI version) or just returning to the
download site (both versions).
Once we have decided to make an official release of the GUI version,
it will no longer be freely downloadable, and it will no longer auto-update. At that time, however,
the command-line version will become non-expiring, free, and open source.
You are welcome to use these versions in the meantime, however I cannot promise any support or
guarantee correctness or accuracy. Use at your own risk. Please send any bug reports to me directly
Macintosh OS X Leopard (GUI version; universal binaries):
Note: After extracting the downloaded file (if necessary), you may need to right-click the icon
and choose Open the first time (to get around the warning that the application is from an unknown developer).
Windows GUI version:
This version has been tested on Windows XP and Windows 7 (both 32- and 64-bit). There may be a few
as-yet-undiscovered glitches in the dialog boxes, so please report these if you encounter them.
Note: After gunzip'ing the downloaded file (if necessary), you may need to make it
executable using a command like chmod a+x paup4a139_osx_leopard.
- Mac OS X:
- Intel Linux:
I am hoping to reduce the number of Linux builds that I provide as executables. For now, here is a binary
for 64-bit Ubuntu. Please let me know (email@example.com) if you cannot run this binary on your system,
and I will try to provide a compatible one.
Version 4.0a139 (current):
This is yet another quick bug-fix release to fix a stupid mistake I made while rushing to get an update ready for
a workshop. The bug was serious; please apply the update. Also check the release notes for previous versions if you
have not already done so..
- Likelihood of models containing both gamma-distributed rates and invariable sites ("+I+G") is calculated incorrectly.
This is a quick bug-fix release to address several issues with maximum likelihood in verison 4.0a137.
Please see the release notes for that version as well.
- Crashes, freezes, or incorrect calculations after changing likelihood models.
- Files output from LScores are no longer compatible with JModelTest and MrModelTest.
- Crashes on the second or later ML analysis using the GTR model.
- The SVDQuartets species-tree method of Chifman and Kubatko is now available (see Chifman, J., and Kubatko, L. 2014.
Quartet inference from SNP data under the coalescent model. Bioinformatics 30:3317–3324.)
- Partitioned likelihood models are now available (from the command line only). Unfortunately, I have not had a chance
to document how to use them, but this will be a high priority, as will dialog-box support for the Mac and Windows versions.
- Likelihood of the "unconstrained" (multinomial) model can now be computed when missing/ambiguous data are present,
using the method of Waddell (2005). This calculation is usually fast, but it might be slow for very large data sets
with a lot of missing data. Consequently, you need to request unconstrained likelihoods as a new option on the
LScores command (or by checking the relevant box in the Tree Scores->Likelihood dialog box).
- Calculation and output of AIC(c) and BIC scores is now supported in the LScores command (Tree Scores->Likelihood
- Taxon labels in plotted trees are now auto-sized based on number of taxa and page size. Once the font size has
been explicitly set by the user, however, it remains in effect for the remainder of the run (or until it is reset again).
Maximum-likelihood bootstrapping has apparently been broken for over a year without me (or
apparently anyone else) noticing it. The problem was so severe that it is extremely unlikely that you would have
accepted the results as valid (in fact you probably would not have even been able to get a run to finish).
However, if you somehow managed to perform an ML bootstrap analysis with any version between 4.0a130 and
4.0a136, you need to repeat the analysis.
- ML bootstrapping fails to run correctly or produces obviously invalid results (see above).
- ML analyses do not always respect character weights intended to be treated as pattern-frequency counts.
- Memory is corrupted, leading to crashes or allocation failures, after changing parsimony character types.
- Tree lists do not handle multiple tokens (e.g., "lscores 2;" works but "lscores 2 5;" does not); bug introduced
at version 4.0a134.
- Statefreqs/Basefreqs command crashes if issued before any other model-based analysis has been performed.
- Option to set number of decimal places for branch-lengths in output treefiles is being ignored.
- Probabilities of state assignments for ML reconstructions (e.g., "lset allprobs; desc/xout=both;") are
not correct for some models (at least G+I)
- Ancestral-state reconstructions under Mk(v) models are not correct.
- Crashes after showing error message for unrecognized option on HSearch command.
- Windows-version: mouse-wheel activity while the recalled command-list is disclosed also scrolls the text
in the main display window.
- Slider controls are not updating the text values in the Windows-version Startup Preferences dialog.
- Output window width is not always in sync with output line length under Windows 7 (but OK under XP).
- Crash when attempting to plot unrooted NJ, bootstrap, etc., trees.
- LSet command output by Automodel includes all 6 components of the 6ST rate matrix. The last "1" causes
the command not to work if pasted back into the command or a file.
- Added "autopart" command and "Automated partitioning" menu command to choose partitioned models a la PartitionFinder.
(Partitioned models are not yet supported in PAUP*, but the output from this command can be used to set up partitioned models
in Garli or RAxML.)
- Added "subtreecolor" command to specify colors on plotted trees for subtrees induced by a list of taxa (OSX version only).
Do "subtreecolor ?;" for syntax (e.g., "subtreecolor red 1-3 5-8;"). Similar commands are available for coloring only the tip
labels ("tipcolor") or both the subtree and the tip labels ("taxcolor").
- The default setting for reading treefiles has been changed to automatic storing of branch lengths and tree weights
unless storeBrLens=no or storeTreeWts=no is explicitly requested. (These options are still useful if treefiles
contain many trees and the branch lengths and/or tree weights are not needed, in which case they
can consume a lot of memory unnecessarily.)
- Added an option to suppress showing of taxon (tip) labels on graphical tree plots.
- Made a few tweaks to graphical tree drawing that arguably improve appearance.
- Output command-line equivalent when optimality criterion is changed from the Analysis menu.
- Restored support for "nowarn" option on ClearTrees command. The option does nothing, but this restores backward
compatibility with old scripts.
- L-BFGS optimizer fails on some data sets with clock models under default (Thorne) parameterization.
- Bootstrap support values written to treefiles were either garbage or associated with incorrect nodes.
- Parsimony analysis crashes with asymmetric stepmatrix characters.
- Optimization of G+I models is incorrect under clock model with some parameterizations.
- Glitches with formatting/truncation of tree scores for output (e.g., pscores); introduced in 4.0a134.
- Crash or other misbehavior after deleting taxa when no trees were in memory.
- Crash with topology constrained distance searches.
- User-input branch lengths are not retained when trees are pruned after deletion of taxa.
- Fixed truncation of user-input branch lengths to integer values when describing trees in the absence of a data matrix.
- SaveDist command ignores "append" option.
- K2P distances were incorrectly calculated as "zero" when the only differences between two taxa were transitions.
This version was not distributed. See release notes for 4.0a136.
- The "automodel" command ("Automated Model Selection" on the Trees menu) is now available. This command emulates
the function of the ModelTest/JModelTest programs without having to run a separate standalone program. Models
may be chosen from one of four model sets (corresponding to those in JModelTest) using the AIC, AICc, BIC,
and DT criteria.
- Additional care is now undertaken when optimizing ML models containing both gamma-distributed rates and
a proportion of invariable sites ("G+I"). Most importantly, an occasional problem is now avoided where ending
at a local optimum causes the likelihood of a more complex model to be worse than that of a simpler model
nested within it.
- Minimum output width is now 100 characters, which requires a display with at least an 800x600 screen
resolution. (I just needed a little more breathing room for some output tables.)
- The long-deprecated "nowarn" option on ClearTrees command has been removed; I assume you wouldn't issue
the command unless you were already sure you didn't want to clear the trees.
- Files containing multibyte unicode characters are being truncated when saved from Mac editor.
- NJ/UPGMA segfaults in command-line version when saving to treefile is requested.
- Interface freezes if a list item is double-clicked in "Show Reconstructions" dialog box on Mac.
- Improve font appearance in Windows version.
- Improve installer and auto-update interface in Windows version.
- "Restore Open Documents" events are now ignored in the Mac version. Previously, documents that were open the last
time PAUP* was quit were triggered to re-opened by the operating system. However, this causes problems for PAUP* when
the default starting mode is "Execute" but the document being re-opened is not an executable NEXUS file.
- Crash occurs while processing character-partitions entered in "vector" format.
- Crash occurs with likelihood if the number of unique site patterns is less than the number of multithreaded tasks.
- "Find" fails in Mac editor if document contains multibyte Unicode characters.
- Setting of gapMode to "newState" from GUI is ignored.
This version was not distributed.
- Fixed crashing when rate matrix parameters for GTR model were estimated by maximum likelihood.
After a bit of soul-searching, I have decided to change the default multithreading setting to be a
single thread. Previously, I queried the system for the number of cores available and defaulted to one thread per
core. The problem with this method is that many machines now have a large number of cores, and using this many
threads degrades rather than enhances performance. Also, on a machine running multiple long jobs, better system
performance is obtained by not having all of these jobs compete for the same set of cores. This is is especially
relevant for jobs running on HPC clusters using the Sun Grid Engine for scheduling--the operating system will
happily report that (say) 16 cores are available even though there are already 15 other jobs running on a node.
So now, if you want to use multithreading for maximum likelihood calculations, you must explicity specify
lset nthreads=n; (where n > 1) before beginning a likelihood analysis (or use the
equivalent setting from the "Optimization" pane of the "Likelihood Settings" dialog box). You will probably want
to do some experimentation to determine the best value for nthreads--two to four may be better than one, but
depending on the size of the data, requesting too many threads will be detrimental. You can also use
lset nthreads=auto; to obtain the old behavior of using one thread per core.
- Balanced minimum evolution is now available for distance analysis, either from the Distance Settings dialog box or by using
"objective=bme" from the DSet command.
- Likelihood scores are now written to score-file in sorted order (unless single-site likelihoods are requested).
- By default, character/taxon partitions and ratesets are now output as lists of character numbers rather than in the previous
"dot-plot" format. The old format is still available by specifying "/dotplot" on the ShowCharPtns, ShowTaxPtns, and ShowRatesets
commands, or by choosing the relevant menu items from the "Show Other" submenu.
- Many internal changes were made in anticipation of support for partitioned likelihood models. I had hoped
support for partitioning would materialize for this release, but there are still too many issues remaining to be
- Fixed problem with output of single-character tree lengths to score-file using PScores (Tree Scores->Parsimony) command
(the lengths for the last tree were output for every tree in the file).
- Fixed crashing or other misbehavior of BaseFreq command ("Base/AA Frequencies" menu command).
- Fixed context-dependent crashing of the Likelihood Settings dialog box.
- Fixed failure to compute a valid kernel agreement subtree (KAST) or Adams consensus tree, due to the same underlying cause.
- Fixed crash after closing "Permutation tests..." dialog box.
- Fixed crash during constrained search if taxa were deleted after a previous constrained search was completed.
- Fixed possible crash while showing histogram from exhaustive search when the number of histogram classes exceeds the range of tree
- Fixed failure to respect the "taxlabmatch=relaxed" setting.
- Fixed possible crash after using DiscardData command (due to failure to reallocate a default ML model).
- Fixed failure of branch-and-bound search to save optimal tree(s) with large-ish data sets.
- Fixed crash with branch-and-bound search under distance criterion.
- Fixed a problem with filtering trees when convexity constraints were in effect.
- Fixed cosmetic glitches in "Evaluate random trees" dialog box.
- Fixed help window popping up if used clicked in the "Base weight" field of the Reweight Characters dialog box.
- Fixed several glitches in Windows-version dialog boxes.
- Fixed glitch in Windows-version Edit menu causing some items to not be displayed.
- "Execute " item in File menu is now updated after a "Save As" to a different name.
- Fixed possible failure of "Find" window in editor not appearing due to being located offscreen.
- Fixed failure to remember previous main window location if it was to the left of the monitor containing the menu bar.
- Fixed possible failure to redefine the "MissAmbig" character set correctly after taxa were deleted.
- Fixed problem with export of data containing characters with multistate taxa with datatype=standard.
- Fixed problems with output of estimated model parameters to tree-score file from LScores.
- Restored compatibility of LScores tree-score file with Shimodaira's CONSEL program.
- Fixed crashing with 2-state (Cavender-Farris) ML models when vectorization was in effect.
- Fixed glitches in graphical tree plots when the default "show as phylogram" setting was changed to "cladogram" (e.g.,
the wrong tree was sometimes shown when multiple trees were stored in memory).
- Fixed crashing with exhaustive search under distance-based optimality criteria.
- Fixed incorrect calculation of likelihoods under Mk(v) model when number of observed states was variable across characters and
molecular clock was enforced.
- Fixed output of patristic distance and homoplasy matrices associated with "DescribeTrees" command.
- Fixed broken Windows-version auto-updater.
- Multiple characters blocks now auto-create a charpartition 'Chars' with subsets defined by block names specified in TITLE commands.
- Charsets can now also be specified as charPtnName.subsetName, where charPtnName is a previously defined
charpartition, and subsetName is the name assigned to one of its subsets.
- Fixed problems with combination of conditional-likelihood rescaling, invariable-sites models, and multithreading. Rescaling was
not being done correctly, with the result that data sets and trees containing larger numbers of taxa were more strongly affected.
- Fixed problems with ancestral-state reconstruction and single-site likelihood calculation when vectorization was enabled.
- Fixed problem in code for checking character partitions that caused ML site-specific rates and partition
homogeneity test to fail.
- Improved robustness of parameter estimation when the model of among-site rate variation includes both gamma-distributed
rates and a proportion of invariable sites.
- Fixed more problems with multiple characters blocks (including cleanup after memory allocation failure).
- Fixed spurious quoting of taxon names when importing FASTA-format files.
- Fixed hang or crash if state-frequencies were estimated under GTR model but rate matrix was fixed.
- Fixed crash if single-site likelihoods were requested with Mkv model.
- Fixed problems saving files with file or directory names containing non-ASCII characters.
- Eliminated memory leak if character or taxa partitions are redefined.
- Editor caret is placed at the beginning of a document created by importing a foreign format, rather than leaving it
at the end of the document.
Yes, I know. The previous version (4.0a126) was a disaster. I decided to add support for multiple Characters blocks in
Nexus input files in order to support (e.g.) Mesquite-generated files that were causing PAUP* to crash. This turned
into a big mess and I had to rush a version out for the European Molecular Evolution Workshop, Several new bugs were
introduced during this period. Unfortunately, I then I got hopelessly busy on
non-PAUP-related projects and couldn't work on the program for a while.
Anyway, the problems fixed in this release include:
With regard to multiple Characters blocks, note that TITLE and LINK blocks created by Mesquite are currently ignored.
If you use multiple Characters blocks, they must conform to a preceding Taxa block (i.e., the same taxa, in the same
order). Eventually I may try to improve support for Mesquite's extensions to the Nexus format, but this is a start.
- Failure to retain charsets, taxsets, etc. following a Data or Characters block.
- Failure to respect the "respectCase" option in the Format command of a Data or Characters block.
- Completely broken likelihood analysis for amino-acid data.
- Crashing when reading in user-supplied distances using a Distances block.
- Crashing of 64-bit versions when reading trees containing output comments (e.g., files output by Garli).
- Minor issues associated with file-selection dialogs.
- %SD values with least-squares distances using weight powers other than 2 were being calculated incorrectly in the
DScores command (but not DescribeTrees).
- Failure to output a consensus tree if it was completely unresolved, and fixed possible problems with showing
a consensus tree when input trees were rooted.
- Crashing in consensus-tree calculation when midpoint rooting was enabled.
- "CountSwaps" command crashing when topological constraints were being imposed.
This version also provides a few additional fixes and improvements:
- Linux and MacOSX/10.5+ builds now contain support for embedded Python. Documentation will come soon.
- In GUI versions, the "ToNexus" command can now be used to import files in formats other than Nexus directly into a
new editor window (by not specifying a "tofile"). Previously, it was only possible to send the converted data to a
- Include-exclude characters dialog box is now much more responsive in Mac version when the number of characters
shown in the lists is extremely large.
- Provided an option for retaining underscore characters in taxon names, charsets, etc., rather than converting to
whitespace (use "Nexus Options" dialog box or "set underscore=[keep|convert];" from the command line).
- Support for import of distance matrices in Phylip and Relaxed Phylip format has been improved. A bug causing
import of Phylip-formatted to fail was fixed.
- Distance matrices may now be exported in either traditional or relaxed Phylip formats.
- Added ability to read user-supplied least-squares weights for distance analysis (arcane for most users).
- Added some new capabilities least-squares distances, including exponential weights and "geometric" versions of
the percent standard deviation statistic (see Waddell et al. 2010,
This build was not generally released..
- Fixed bug in AU test that could cause incorrect P values, crashes, or freezes in cases where a candidate tree was never the best
tree in any bootstrap replicate. It appears that in most cases, the effects of the bug were inconsequential, causing a small P value
to be reported as a different small P value (often within the range of the bootstrap error variance). However, it is possible that
it could have caused more serious errors, and rerunning any analyses that may have been affected is recommended.
- Improved speed of storage and retrieval of large numbers of trees by using better hashing strategies.
- Fixed some problems with inability to open files using relative pathnames in file specifications.
- Added a new mode to the "CD" command: "CD *;" from an active input file explicitly sets the current
working directory to the directory containing this file.
- The default setting for handling character weights in bootstrap analysis has been changed to the more natural "treat as repeat
counts" option. Note that this option cannot be used if character weights take noninteger values; in that case an error message will
now be issued unless one of the other options for weight-handling is specified.
- Added "taxcolor" command to specify colors for taxon labels on plotted trees.
- Import of relaxed-Phylip format data files now works correctly with taxon names longer than 10 characters.
- GammaPlot command no longer requires a data matrix (which was silly).
- Tree storage is now more efficient when a substantial number of the original taxa have been deleted.
- Fixed bogus error message that agreement-metric tree distances could not computed because one or more taxa were missing
from the tree, when taxa had indeed been deleted but the tree contained only non-deleted taxa.
- Fixed crash with ML distances and 6ST substitution models.
- Fixed crash with bootstrap under distance criterion when using ML distances.
- Fixed possible hang if a calculation thread completed while ab error message alert was active (unlikely, but possible).
- Eliminated spurious message about uninformative characters not being included in Goloboff
scores in output of parsimony scores for individual characters, when Goloboff weighting was not in
- Eliminated spurious message about constant characters being ignored under Mkv model when criterion was not likelihood.
- Fixed output glitches with Goloboff-parsimony tree scores (showing of too many decimal places, failure to show tree lengths when
Goloboff parsimony was active).
- Fixed possible crash if more than 255 characters were typed into the Mac-version command line.
- Fixed possible crash with ABC tree-to-tree distances if an input tree was a star tree or if more than 128 taxa were present
and at least one input tree was nonbinary.
- Fixed incorrect output of command-line equivalent when "UPGMA" was chosen as the search method in the "Bootstrap/Jackknife"
- Fixed incorrect jackknife sampling when character weights were present and the "simple" option for weight handling was requested.
- Catch user-entered tree-number of "0" as an error, rather than crashing.
- Fixed problem with scoring of distance trees containing negative branch lengths (introduced in 4.0a124).
- Removed some debugging output accidentally left enabled.
- The "usertree" command is now available. It can be used to quickly input a single tree without having to deal
with the complexity of a full Trees block.
- Importing of distance matrices in Phylip and relaxed Phylip format is now supported.
- Alphanumeric names are now recognized in tree lists when trees have non-integer names (the integer number
can still be used).
- Exporting to Phylip (character-data and distances) now replaces blanks with underscores appropriately, depending
the context (tree descriptions vs. data/distance matrices)
- Switched to "Meslo LG" as the main display and default editor font--Apple's Menlo Regular font had
problems with the width of the '%' glyph as well as some other undesirable features, and the previously used
Deja Vu Sans Mono had issues with the hyphen (too short) and the tilde character (not curvy enough to be
easily distinguishable from a hyphen).
- Tightened up Print/Preview Tree(s) code, trying to fix an elusive crashing bug reported by users that I
haven't been able to reproduce.
- More "under the hood" work in preparation for partitioned/mixture models (hopefully this didn't break anything)
- Fixed some minor interface issues:
- incorrect radio-button titles in Gaps panel of Parsimony Settings dialog (Windows version only)
- cursor remaining as watch cursor after cmd-S in Mac editor
- better error diagnostics when end-of-file is reached unexpectedly while executing a file
- The Macintosh OS X editor has been completely rewritten for OS X Leopard and later (now based on the Cocoa
NSTextView class rather than the buggy and poorly supported Multilingual Text Engine [MLTE]). Improvements
- support for Unicode text
- fast search and replace
- ability to handle arbitrarily long lines
- elimination of problems involving tabs
- user-selectable fonts
- zippier performance in general
- Added calculation and output of the "Kernel Maximum Agreement Subtree" (KAST) along with previous agreement
subtree calculations. The KAST is the subtree containing only those taxa found in every optimal agreement subtree.
- Added "Defaults" buttons to "Import Data", "Export Data", and "Get Trees", and "Save Trees" dialogs so that users
can choose their own preferences for the default settings.
- Changed the command-line flags for Unix and Mac command-line versions, going to a more standard POSIX/Gnu-like
system. This may break some people's scripts that use the old flags for starting PAUP*, but it just had to be done.
You can run start paup with the -h or --help flags to get a summary of the options, and modifying the script to use
the new syntax should be trivial.
- Added command-line argument support for invoking the Mac GUI version of PAUP* from the prompt in a terminal window
or from a script. (Ordinarily, you would just use the non-GUI version instead, but there are circumstances
where the ability to invoke the GUI version without relying on the Finder is handy.)
- Multithreading is now working for ML calculations in the Windows version.
- Fixed possible crashes or other problems with heuristic searches under likelihood after using the DescribeTrees
- Fixed non-responsiveness of user-interface during long tree-sorting operations.
- Fixed "Export Distances" not respecting user-modified default settings.
- Fixed crashing in ML ancestral-states reconstruction with gamma-distributed rates and joint (rather than marginal)
- Fixed incorrect drawing of the same tree repeatedly in the Preview Trees window when multiple trees were shown
on each page, after changes to option settings that resulted in the trees being redrawn (but without branch-length
reoptimization, rerooting, etc.).
- Fixed obvious problems with Cavender-Farris (2-state) model when vectorization was enabled.
- "Root Trees" and "Condense Trees" dialogs were not appearing when selected from the menus due to the inadvertent
ommission of their code from the application bundle.
- Fixed interface problem involving line termination settings for exported files.
- Fixed crashing of 'ToNexus' command when issued from Mac or Windows GUI version.
- Fixed crash starting Preview Trees if optimality criterion was set to likelihood and user branch lengths were in
effect at the time the dialog was opened.
- Fixed hang in heuristic search dialog box associated with the "chuckscore" entry.
- Fixed problems with the "DCollapse" option in distance analysis.
- Fixed output of SS, Weighted SS, and APSD distance scores when input distances are tiny.
- Resolved a few issues with import and export of FASTA and MEGA file formats.
- Fixed showing of document icons.
- Resolved some printing issues on Windows version.
- Treefiles in raw Newick format (e.g., those used and created by MEGA and Phylip) are now handled by the GetTrees
- Nexus treefiles are now accepted without a terminating "End;" signifying the end of the block. (E.g., this allows
treefiles from active MrBayes runs to be read in without having to edit them to add the end statement.)
- Requesting interpretation of trees as rooted or unrooted may now be done from the "Get Trees" dialog box (e.g.,
trees from MrBayes treefiles can be read in as unrooted even though they are identified as rooted trees inside the
- Fixed failure to write "#NEXUS" reliably at the beginning of saved treefiles.
- Tree numbers for preview/print are now valid when trees from a file are combined with trees in memory.
- Export of data to relaxed Phylip format now converts spaces in taxon names to underscores.
- FASTA-format export now works correctly.
- FASTA-format input changed so that only spaces or newlines break the sequence-name token (and names are quoted
appropriately if they contain special characters).
- Fixed hang or other misbehavior when optimizing GTR rate-matrix parameters along with clock constraint.
- Fixed possible crash when describing trees with branch-length table under likelihood criterion.
- Fixed crash and/or bogus status output after exporting files in MEGA format.
- Changed "allowpunct=yes" to apply to TaxLabels command as well as to names in data matrix.
- File name for PDFs and Windows metafiles generated from Preview/Print Trees is now remembered between
Version 4.0a120 just extends the expiration date to 1 Feb 2012 to avoid possible end-of-semester
unpleasantness for those using it in courses (a119 and a120 are identical otherwise).
- Menu/dialog interface for Windows version is essentially complete!
- Updated MEGA import to support modern versions of MEGA; MEGA export is now also supported.
- Added support for import and export of "Relaxed PHYLIP" file format (used by RAxML and PhyML).
- Added support for import and export of FASTA files.
- Finally fixed the bug that caused saving of files from the editor to quietly fail. (I had previously
not been able to reproduce reports of this bug, but was able to track down and fix it after seeing it happen
during a workshop demo.)
- Fixed crash (introduced at 4.0a117) when calculating likelihoods for DNA data containing partial ambiguity codes
(including but not limited to 'X').
- Fixed crash if KH and AU tests were both requested, but SH test was not also requested.
- Topological constraints are no longer permitted in star decomposition searches (it was buggy, and so unuseful
and ineffective that it wasn't worth fixing the bugs).
- Windows version is now built with stating linking to the C library, hopefully solving problems with missing
DLLs on some systems (typically XP, but I don't know how general the problem is).
- Fixed possible memory corruption after importing of a PHYLIP file failed due to improper formatting.
- By popular request, file filtering on "Open" file-selection dialogs now defaults to "Open all files".
This makes it easy to open files in the editor that you should not ever attempt to edit, so be careful.
Note: There were serious problems with the Kishino-Hasegawa test in versions 4.0a112-4.0a114
(introduced accidentally while implementing the AU test). Please repeat any analyses involving KH tests
performed using these versions before publication!
- The Mk model is back (after a very long departure)! Likelihoods for non-sequence data can now be computed
following Lewis (2001; "A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data";
Systematic Biology 50:913-925).
- Fixed several issues with ML reconstruction of character-states using Reconstruct and MPRSets commands.
- Fixed issues with scrolling and pause/resume in GUI-version output window.
- Fixed several issues related to ML multithreading modifications introduced in version 4.0a115:
- Fixed crash in SaveTrees command if branch-lengths were requested when criterion was likelihood.
- Fixed crash in Condense command when criterion was likelihood.
- Fixed crash in tree preview if "show branch lengths" was checked when criterion was *not* likelihood.
- Not publicly distributed.
- Fixed inaccurate calculation of likelihoods for models including an invariable-sites category, when multithreading
was being used and data set was large enough that conditional-likelihood rescaling was needed (bug in 4.0a115 only).
- Fixed memory-allocation problem in Windows version that caused crash in branch-and-bound and exhaustive searches.
- Made a change that will hopefully eliminate anomalous behavior (e.g., reverting to an earlier version) when saving
files from the Mac OS X text editor. I wish I could be more confident, but I have found it very difficult to
reproduce this bug.
- Fixed disappearing scrollbar glitch in OSX GUI version.
- Fixed crashing of the PairDiff command.
- More Windows-version dialog boxes.
- New feature: A new tree-to-tree distance measure is now available, a metric described most
accessibly by Lin, Rajan, and Moret (2011; "A metric for phylogenetic trees based on matching"; Proc. 7th Intl. Symp.
Bioinformatics Research & Appls. ISBRA'11, Lecture Notes in Computer Science 6674; Springer Verlag). This method
is a rediscovery of an identical method published by Bogdanowicz (2008; "Comparing phylogenetic trees using a minimum
weight perfect matching"; Proceedings of the 2008 1st International Conference on Information Technology,
IT 2008 19-21 May 2008, Gdansk, Poland). This metric has very nice properties relative to the widely used symmetric-
- Overhauled multithreading for ML calculations, resulting in significantly better scaling with number of processors
for most data sets.
- Overhauled SSE2/Altivec vectorization for ML calculations, resulting in noticeably faster run times.
- Calculation of all pairwise distances between trees using the Robinson-Foulds distance are now significantly
faster for large trees and/or large collections of trees, due to incorporation of some elements of the algorithm
described by Sul, Brammer and Williams (2008; "Eﬃciently Computing Arbitrarily-Sized Robinson-Foulds Distance
Matrices"; Algorithms in Bioinformatics: 8th International Workshop, WABI 2008, Karlsruhe, Germany).
- Fixed a number of problems involving thread-safety that I believe explain the source of mysterious, seemingly
random and difficult-to-reproduce, crashes.
- "Print/View Consensus Trees" menu item was inadvertently disabled if input trees for consensus were rooted
(bug in 4.0a114 only).
- Fixed crash when doing KH test unless SH or AU test was also requested.
- Fixed crashing as well as other problems associated with the "save N best trees" option in heuristic searches.
- Fixed a few more issues with updating of tree preview window after changes to the settings (especially
involving switching between one tree/page and multiple trees/page).
- Restored "Save tree scores to file" functionality in "Exhaustive Search" dialog box.
- Fixed output of tree-score frequency-distribution to file with exhaustive search and random-tree evaluation.
- Fixed some problems with search-and-replace in the OS X text editor (but possibly not all of them).
- Fixed incorrect branch lengths for trees saved to file (bug introduced in 4.0a113 while fixing a different bug).
- Fixed showing of internal branch support as "0" when bootstrap trees were rooted using a monophyletic outgroup.
- Fixed crash when saving consensus-trees to file while midpoint rooting was in effect.
- Fixed crash with Parsimony Scores (PScores) command with rooted trees.
- Fixed hang with find-and-replace in editor (find-and-replace is still much slower than I'd like, but I'm more
or less at the mercy of the Apple libraries)
- Fixed problem with Page Setup in Tree Preview window under OS X 10.5 (Leopard).
- Fixed bogus complaint about missing taxa when attempting to compute consensus tree from treefiles with no
- Added option for keeping each edge segment as a separate object in graphical tree plots exported as PDF files.
The advantage is that each segment can be individually selected after importing these files into graphics programs
such as Adobe Illustrator. The downside is that the joints between connecting segments may not be as clean.
- Random trees can now be generated under topological constraints (previously this capability was only available
when generating all possible trees)
- Added capability for generating trees by permuting taxon labels on a fixed topology (GenerateTrees command).
- Fixed inability to handle very long file/path names in "File=filename" subcommands (e.g., GetTrees)
- Fixed a couple of memory-management problems that could potentially causes crashes.
- Fixed problems with truncation rather than rounding of bootstrap proportions on graphical tree plots, as
well as failure to respect setting of number of decimal places
- Fixed a crash when consensus trees or agreement subtrees were rooted using midpoint rooting but no character
data were available.
- Fixed startup crashes related to Python on systems lacking the expected version of Python,
primarily on OS X 10.5 (Leopard).
- Fixed crashing during majority-rule consensus tree calculation.
- Fixed failure to include gapped characters in the 'missAmbig' predefined character set.
- Added support for AU test to OS X GUI
- (Finally) fixed cursor handling in dialog boxes so that it switches between arrow and
Version 4.0a111 notes
A few bug fixes, plus Shimodaira's AU test availability.
Specific changes since 4.0d110 include:
- Shimodaira's Approximately Unbiased (AU) test for comparing trees is now available
- Fixed incorrect initialization of predefined 'gapped' and 'missambig' character-sets
(accidentally broken in 4.0a110 only).
- Dragging of Finder icons to main display window is now working again (opens file in editor
unless shift key is pressed)
- Fixed problems with updating of user-defined branch lengths after pruning of deleted taxa.
- ML with R-Y (two-state) recoded DNA data is now faster for huge alignments (> 10^6 sites).
Version 4.0a110 notes
Once again, mostly just bug fixes, but stay tuned.
Specific changes since 4.0d109 include:
- Fixed completely broken output of bootstrap support values in trees saved from the SaveTrees
(Save Trees to File) command.
- Added support for saving majority-rule support values to treefiles output from the Contree
(Compute Consensus) command (SaveSupport=Brlens|NodeLabels|Both)
- Fixed output of trees in matrix representation when input trees do not all contain the full
set of taxa. Now, missing values are used in this case, allowing simple automation of MRP
supertree construction--just input the set of trees (each of which may contain only a subset of
the full set of taxa), generate the matrix representation, execute the resulting file, and do a
- Fixed incorrect output of user-defined branch lengths to saved treefiles.
- Fixed opening of Distance Settings dialog in a window that was much too large.
- Fixed possible hang when midpoint rooting was requested from a Rooting Options dialog invoked
from the Preview Trees window.
- Fixed an issue with "gapmode=newstate" and user-defined stepmatrix types.
- Fixed failure to start log file if the "save current contents of display buffer to log file"
option was requested.
- Improvements in tree printing
- Fixed drag-and-drop of document icons to Finder icon and dock (still need to allow dragging
directly to PAUP output display window).