NAME

       kalign - Global and progressive multiple sequence alignment

SYNOPSIS

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

DESCRIPTION

       Kalign (3.3.4)

OPTIONS

       --format
              : Output format. [Fasta]

       --type : Alignment type (rna, dna, internal). [rna] Options: protein, divergent (protein)

              rna, dna, internal (nuc).

       --gpo  : Gap open penalty. []

       --gpe  : Gap extension penalty. []

       --tgpe : Terminal gap extension penalty. []

       -n/--nthreads
              : Number of threads. [4]

       --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