get4foldSites: returns 4-fold degenerate sites from fasta files.
Author: B. Nevado
Usage:
Usage: get4foldSites -infile in.txt -outfile res.fas -iupac 0/1 -verbose 0/1
-infile: text file with list of input fasta files to process (1 file per line).
-outfile: output fasta file to write to.
-iupac: if set to 1 will consider positions with 'diploid' IUPAC codes.
Output: 1 fasta file with all 4-fold sites found across all input files.
Notes:
Tested on linux with g++ v5. Earlier version (4.8) did not work.
Set '-verbose 0' to turn off warnings.
Installation (Linux):
git clone https://github.com/brunonevado/get4foldSites.git
cd get4foldSites
make
./get4foldSites
Folders:
/bin : executable compiled for Linux, static
/source: source code
/examples: test/example files, run with get4foldSites -infile infiles.txt -outfile out.4fold.fas -iupac 1 -verbose 1