run_neighbor - run Phylip's 'protdist' program through Bioperl
run_protdist [-i inputfile] [-o outfilename]
Provide an alignment file to run protdist on. File should be named either .aln or .phy. This is required so that we can determine if we need to convert a clustalw alignment into phylip. You are welcome to extend the script to work on other MSA formats which bioperl supports. This is intended to be used in very simple manual pipelines.
The input file should be named in the form of file.phy or file.aln the program expects a file in the form of (\S+)\.(\S+).
This will run the application 'protdist' using the 'KIMURA' formula to build a a protein distance matrix. Those with phylip3.6 will want to make some changes if they want to use JTT. I'm happy to help add this in as a cmd-line argument if it is requested.
Jason Stajich, jason-AT-open-bio-DOT-org