my scripts for IGB related projects
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S2G.py - a script for joining satellite sequences according to "scheme" file. As input it takes fasta file with satellite sequences and scheme file representing their relative positions in a genome; the script outputs satellite sequences concatenated according to the scheme file.
- scheme.txt - an example of scheme file
- satellites.fasta - an example of satellites file
- genomes.fasta - output example
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Population genetics scripts
- make_standard_table.R reads genalex formatted file and outputs a table like:
Locus Pop N.alleles H.exp H.obs AR ... ... .......... ...... ...... ... Mean ... .......... ...... ...... ... SE ... .......... ...... ...... ... Total ... .......... ...... ...... ... - get_pop_diff.R reads genalex formatted file and outputs Gst (both by Hedrick and Nei) and Jost's D as tables (tab-delimited) along with NJ trees built using Gst/D distances (in nwk and png formats)