FASTA alignment by species fasta_concatenate_by_species.py $input1 $out_file1

**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 .. class:: warningmark This tool will only work properly on files with Galaxy style FASTA headers.