9 name=${BASH_REMATCH[1]}
11 /usr/local/bin/mafft --keeplength --add $i CDS_aligned_partials_MAFFT_merged_ni.fasta > REF_PLUS_Q_${name}.fasta
18 /home/zma/SOFTWARE/PHYLO/PPLACER/PPLACER11ALPHA19/pplacer-Linux-v1.1.alpha19/pplacer -m GTR -t RAxML_bestTree.CDS_aligned_partials_MAFFT_merged_GTR -s RAxML_info.CDS_aligned_partials_MAFFT_merged_GTR REF_PLUS_Q_${name}.fasta -o PP_Q_${name}.json
25 /home/zma/SOFTWARE/PHYLO/PPLACER/PPLACER11ALPHA19/pplacer-Linux-v1.1.alpha19/guppy sing PP_Q_${name}.json