Provided by: augustus_3.3.3+dfsg-2build1_amd64 bug

NAME
       prepareAlign - prepare an alignment for block profile creation by deleting gap-rich rows


SYNOPSIS
       prepareAlign < input.fa  > output.fa


DESCRIPTION
           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.


AUTHORS
       Oliver Keller

                                                                                  PREPAREALIGN(1)