astral_pipeline

ASTRAL

#Align

awk '{print "mafft",$1".faa",">",$1".aligned.faa"}' 26_align.sh > 26_aligner.sh

module load mafft/7.471

mafft OG0003652.faa > OG0003652.aligned.faa

..

#Fasttree

awk '{print "fasttree",$1".aligned.faa",">>","26.tre"}' orthos.txt > 26_fasttree.sh

Conda activate fasttree

fasttree OG0003652.aligned.faa >> 16.tre
...


Renaming

#!/bin/bash
readarray list < alignments.txt
for i in ${list[@]}
  do
  cat $i | awk -F \| '{print $1,$2}' > ${i/.aligned.fa/.aln}
  wait
done


#ASTRAL

module load java/14

java -jar ../../Astral/astral.5.7.5.jar -i 16.tre -o 16.astral.tre 2>16astral.log