CALCD_FROM_FAS: Calculates Patterson's D-statistic from a set of aligned fasta files.

Author: B. Nevado

Usage:
calcD_from_fas -folder /home/data -contigs all_contigs.txt -tests tests.txt -outfile result.txt -allsites 1/0
-folder: folder containing fasta files.
-contigs: list of contigs within 'folder' to use in test.
-tests: tests to perform, each line should contain sequence names to use (comma separated, order: H1,H2,H3,Out; lines starting with # are ignored).
-outfile: file to write results to.
-allsites: if 1, will use all sites from all files. if 0, will use only first abba/baba site from each fasta file.
-strict: if 1, will stop with an error if a species is missing in any fasta file. If 0, will skip that file.

Output: text file (to -outfile) with number of abba and baba sites, D-statistic, and Z-score.

Notes:
Positions with unknown bases are ignored.

Installation (Linux):
git clone https://github.com/brunonevado/calcD_from_fas
cd calcD_from_fas
make
./calcD_from_fas