This is the command bp_run_protdist.plp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
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.
Use bp_run_protdist.plp online using onworks.net services