1) UNIX Shell Script for Mass Alignments using Muscle

This is a simple shell script for running muscle with one or more alignment automatedly.

Muscle.sh

Process Code

for i in xx*
do
muscle -in $i -out $i"_align".fasta
done


Usage Notes:

1) All your fasta files that are required for alignments must have xx1,xx2,etc included in the file name.

2) Your output files would have "_align" included in the file name.

Code by: BenBen
Blog Post by: BenBen
Post Edited by: BenBen