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99.scripts/workflow/orthology_inference/06.trim_alignment.sh

@@ -0,0 +1,8 @@
+#! /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"