Datasets and results files for are available under their respective models.
The jrna Perl library parses alignments (they need not be RNA) and returns input files for use in popular analysis programs and/or html-based reports regarding the composition of the given datasets. See help for more information. Releases are available here. Please read the __README upon download. 03/01/05 - Note that the jRNA scripts are being replaced by 'Psy', a more programmer friendly and powerful set of matrix handling tools. Estimated release date summer of 2005.
Jrna sample template
An example template file that can be used with the Jrna.pm library.
Various small perl scripts that probably represent functions available elsewhere. Version numbers are stored in the script file. Use with caution and double check that your results make sense.
For use with PHASE 1.1. Note that PHASE 2.0 is apparently coming soon, and these scripts might become redundant!
- phase2nexus.pl Converts PHASE tree output to a PAUP treefile. The file does not include a taxa or data block, these blocks must be loaded from a PAUP datafile (use Jrna to make a nexus file with the same partitions and execute this file first). Executing the file output by the script in PAUP generates a majority rule consensus tree which is automatically saved to the file 'phase_consensus.tre'. This result is then comparable to results generated in MrBayes.
Usage: 'perl phase_to_nexus.pl <phase .samples file (treefile)> <phase .output file> <name of nexus file to be made- don't include '.nex'> <burnin (for no burn-in use 1)>'
e.g. 'perl phase2nexus.pl phase_results.samples phase_results.output my_results 1'
- phase2tracer.pl Loads PHASE 1.1 output files and returns a file of samples file similar to that generated by MrBayes. This file can be loaded into Tracer, a handy program of use in examening parameter convergence.
Usage: 'usage: 'perl phase2tracer.pl <phase filename root> <output file name> <step size>'
e.g. 'perl phase2tracer myphasedata phaseresult.txt 100'
PHYLIP to flat
phy2flat.pl Perl script converts interleaved Phylip formatted files to a single large interleave.