Concaterpillar

Concaterpillar is a hierarchical likelihood-ratio test for phylogenetic congruence. The most recent version of Concaterpillar, implementing MPI-based distribution of subprocesses, can be downloaded here. You can also get the users' manual.

Features added:

Concaterpillar versions 1.7.2 - 1.8a:

• These versions and subsequent versions will be hosted at Jessica Leigh's site here.

Concaterpillar 1.5:

• Removed -a and -r steps... these are now integrated in -t
• Support for RAxML 7.2
• Uses the subprocess Python module (availble in Python 2.5 on: for older Python installations, you'll need Concaterpillar 1.4)
• Fixed some MPI cleanup problems

Note to MPI users: We will be migrating to mpi4py shortly, rather than pyMPI, as pyMPI has not been updated in several years

A Windows version of Concaterpillar v1.4 is available upon request from the author by emailing jessica{dot}w{dot}leigh{at}gmail{dot}com. While windows is not officially supported a poorly tested version is available due to user requests.

Concaterpillar 1.4:

• support for nucleotide alignments
• pre-screening to make sure that all alignment pairs have enough taxa in common
• added a debug flag (-d, --debug) to print out all output from RAxML in case users are experiencing problems
• added a cleanup step to remove old RAxML output files that might cause subsequent runs to crash (user will be asked before files are deleted)
• added an optional flag to allow Concaterpillar to old RAxML output files without asking (-n, --noask)
• support for "relaxed" Phylip alignment format (not strictly 10 characters per sequence name)

Concaterpillar 1.3:

• fixed some bugs that might be encountered if some of your alignments have extremely different true phylogenies (thanks to Haruo Suzuki for finding this)

Concaterpillar 1.2:

• trees are inferred and evaluated using RAxML (faster and more accurate)
• an improved algorithm for resuming interrupted runs has been implemented
• an installation script has been added to locate programmes on which Concaterpillar depends
• support for more substitution models has been added

If you use Concaterpillar for a publication please cite:

Leigh JW, Susko E, Baumgartner M, Roger AJ. Testing congruence in phylogenomic analysis. Syst Biol. 2008 Feb; 57(1): 104-15.

The version of Concaterpillar used for this publication is available here.