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

Bugs we are still intending to work on and haven't yet fixed

 

Recently fixed bugs

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 your version.

version 3.698 (October, 2019)
A serious problem arose due to recent changes in Microsoft Windows. Here is the background and some suggested workarounds:

For the two tree-plotting programs (Drawgram and Drawtree) the Java environment that we use to develop the front end ended up making Java code that calls a compiled C program that is in a Dynamic Link Library (DLL). Originally that program was 32-bit code that would run on Windows systems that were either 32-bit or 64-bit.

Lately, however, the Java systems installed on Windows were only willing to run 64-bit executables. And only willing to look for those executables in DLLs that contain 64-bit compiled code. But the compiled executables for Windows for 3.695 make 32-bit code, put it in the DLLs, and put those in a different folder than Java looks at. So the "path" Java uses is wrong.

I finally managed to recompile the code so as to have everything be 64-bit code. So everything works in version 3.698. Our downloads page now has both a Windows 64-bit version and a Windows 32-bit version available.

If you can't install those for some reason, here were some possible work-arounds:

  1. Find an old Windows system that is happy with 32-bit executables and whose installed Java is happy with 32-bit code in DLLs, and install PHYLIP and run it there.
  2. Move your tree to a MacOS system and have PHYLIP installed there. It should run correctly there.
  3. Move your tree to a Linux system and have PHYLIP installed there. It should run correctly there.

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)
version 3.69 (September, 2009)

version 3.68 (August, 2008)
version 3.67 (July, 2007)

version 3.66 (August, 2006)

version 3.65 (August, 2005)

version 3.64 (July, 2005)

version 3.63 (December, 2004)

version 3.62 (September, 2004)

version 3.61 (August, 2004)

version 3.6 (July, 2004)

version 3.6b (July, 2003)

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.

version 3.6a3 (July, 2002)

version 3.6a2.1
A quick correction of 3.6a2 since:
version 3.6a2 (July, 2001)
These bugs which were present in version 3.6a were corrected
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:
version 3.573

version 3.572

version 3.57
versions 3.56

versions 3.54 and some executables of 3.55


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