rbh.pl

Finds reciprocal-best-hit single-copy matches between two al-by-all BLAST searches

It will find the reciprocal-best single-copy genes between two sets of BLAST outputs in format 7. If FASTA files are provided it will generate FASTA files with the sequence pairs found. It will also generate a list of gene names. A threshold for e-values can be provided using the -filter argument.

Installation

git clone https://github.com/santiagosnchez/rbh
cd rbh
chmod +x rbh.pl
sudo cp rbh.pl /usr/local/bin

Running the script

Run with -h for more details.

perl rbh.pl -h

USEAGE:

perl rbh.pl -blast1 <blast_output_tab_1> \
            -blast2 <blast_output_tab_2> \
            -fasta1 <file_1.fasta> \
            -fasta2 <file_2.fasta> \
            -outdir <pairs> \
            -outfile <outfile> \ 
            -filter <e-value> \

Example:

perl rbh.pl -bast1 sp1_BLAST.txt -bast2 sp2_BLAST.txt -fasta1 sp1_seqs.fasta -fasta2 sp2_seqs.fasta -outdir my_rbh -outfile myout_rbh.txt -filter 0