The current protocol is especially useful for people with limited computational skills. However, some procedures may become laborious or exceed the capacity of the software when handling a large number of sequences. These bash commands can be used to perform indicated procedures more easily on macOS Terminal or Ubuntu subsystem for Windows.

#Procedure B Multiple Sequence Alignment using MAFFT
mafft --auto --keeplength --maxambiguous 0.01 --addfragments othersequences.fasta referencesequence.fasta > MSA.fasta

#Procedure D Selection of ROI (replace START and LENGHT of ROI)
awk 'BEGIN{RS=">";FS="\n"}NR>1{seq="";for (i=2;i<=NF;i++) seq=seq""$i; print ">"$1"\n"substr(seq,START,LENGTH)}' MSA.fasta > ROI.fasta

8/24/2021 3:32:56 PM Reply