NAME

       kalignfmt - Global and progressive multiple sequence alignment

SYNOPSIS

       kalignfmt-avx2 -i <seq file> -o <out aln>

DESCRIPTION

       Kalign (3.3.4)

OPTIONS

       --format
              : Output format. [Fasta]

       --reformat
              : Reformat existing alignment. [NA]

       --changename
              : Change sequence names to 1 .. N. [NA]

       --unalign
              : Remove gaps and write to fasta. [NA]

       --clean
              : Perform additional checks on alignment. [NA]

       --version (-V/-v)
              : Prints version. [NA]

EXAMPLES

       Passing sequences via stdin:

              cat input.fa | kalign -f fasta > out.afa

       Combining multiple input files:

              kalign seqsA.fa seqsB.fa seqsC.fa -f fasta > combined.afa

COPYRIGHT

       Copyright © 2006,2019,2020,2021 Timo Lassmann

       This program comes with ABSOLUTELY NO WARRANTY; for details type: `kalign -showw'.
       This  is  free  software, and you are welcome to redistribute it under certain conditions;
       consult the COPYING file for details.

   Please cite:
              Lassmann, Timo.  "Kalign 3:  multiple  sequence  alignment  of  large  data  sets."
              Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795