What it does

This tools attempts to parse FASTA headers to determine the species for each sequence in a multiple FASTA alignment. It then linearly concatenates the sequences for each species in the file, creating one sequence per determined species.

Example

Starting FASTA:

>hg18.chr1(+):10016339-10016341|hg18_0
GT
>panTro2.chr1(+):10195380-10195382|panTro2_0
GT
>rheMac2.chr1(+):13119747-13119749|rheMac2_0
GT
>mm8.chr4(-):148269679-148269681|mm8_0
GT
>canFam2.chr5(+):66213635-66213637|canFam2_0
GT

>hg18.chr1(-):100323677-100323679|hg18_1
GT
>panTro2.chr1(-):101678671-101678673|panTro2_1
GT
>rheMac2.chr1(-):103154011-103154013|rheMac2_1
GT
>mm8.chr3(+):116620616-116620618|mm8_1
GT
>canFam2.chr6(+):52954092-52954094|canFam2_1
GT

becomes:

>hg18
GTGT
>panTro2
GTGT
>rheMac2
GTGT
>mm8
GTGT
>canFam2
GTGT

This tool will only work properly on files with Galaxy style FASTA headers.