#! /usr/bin/env bash
mkdir -p trimed_nal
echo -n > trimal.cmds
for i in cds_aln/*.nal ;do
    j=$(basename "$i")
    echo "trimal -in $i -out trimed_nal/${j/.nal/.trimed.fa} -automated1 -resoverlap 0.5 -seqoverlap 50" >> trimal.cmds
done
xargs -t -P 4 -I cmd -a trimal.cmds bash -c "cmd"