prepareAlign - prepare an alignment for block profile creation by deleting gap-rich rows
prepareAlign < input.fa > output.fa
An input multiple alignment of proteins is read from standard input. prepareAlign removes rows from it with the aim of producing fully conserved blocks in the remaining alignment which is then output to standard output.
When an alignment contains many sequences and too many gaps, e.g. a full PFAM alignment, trying to run msa2prfl.pl results in the message "No blocks found in MSA". Then use "prepareAlign" first to eliminate sequences.