How do I run pal2nal.pl in batch mode ?
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3 days ago
Ramana • 0

HI,

I had more than 4,500 orthologs, how do I run pal2nal.pl in batch mode. by taking two input files ?

pep.aln - OG0016582.mt.r.py.fa
nuc.fasta - all_OG0016582.fa.cds.fa 


pal2nal.pl aafasta/OG0016582.mt.r.py.fa  cdsfasta/all_OG0016582.fa.cds.fa -output paml > all_OG0016582.paml.fasta 

I wrote a script, can some one correct my script, thanks.

for i in $(ls -1 *.fa | sed 's/\.fa//'); do  pal2nal.pl  aafasta/$i\.fa  cdsfasta/$i\.fa -output paml > $i\.fasta ; done
gene genome protein • 149 views
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