1BP_RUN_PROTDIST(1) User Contributed Perl Documentation BP_RUN_PROTDIST(1)
2
3
4
6 run_neighbor - run Phylip's 'protdist' program through Bioperl
7
9 run_protdist [-i inputfile] [-o outfilename]
10
12 Provide an alignment file to run protdist on. File should be named
13 either .aln or .phy. This is required so that we can determine if we
14 need to convert a clustalw alignment into phylip. You are welcome to
15 extend the script to work on other MSA formats which bioperl supports.
16 This is intended to be used in very simple manual pipelines.
17
18 The input file should be named in the form of file.phy or file.aln the
19 program expects a file in the form of (\S+)\.(\S+).
20
21 This will run the application 'protdist' using the 'KIMURA' formula to
22 build a a protein distance matrix. Those with phylip3.6 will want to
23 make some changes if they want to use JTT. I'm happy to help add this
24 in as a cmd-line argument if it is requested.
25
27 Jason Stajich, jason-AT-open-bio-DOT-org
28
29
30
31perl v5.8.8 2007-04-19 BP_RUN_PROTDIST(1)