NAME

       spoa - SIMD partial order alignment tool

SYNOPSIS

       spoa [options ...] <sequences>

DESCRIPTION

       Spoa  (SIMD  POA) is a c++ implementation of the partial order alignment (POA) algorithm (as described in
       10.1093/bioinformatics/18.3.452)  which  is  used  to  generate  consensus  sequences  (as  described  in
       10.1093/bioinformatics/btg109).  It  supports  three  alignment  modes:  local  (Smith-Waterman),  global
       (Needleman-Wunsch) and semi-global alignment (overlap).

OPTIONS

       <sequences>

              input file in FASTA/FASTQ format containing sequences

   Optional

       -m, --match <int>

              default: 5 score for matching bases

       -x, --mismatch <int>

              default: -4 score for mismatching bases

       -g, --gap <int>

              default: -8 gap penalty (must be negative)

       -l, --algorithm <int>

              default: 0 alignment mode:

              0 - local (Smith-Waterman) 1 - global (Needleman-Wunsch) 2 - semi-global

       -r, --result <int>

              default: 0 result mode:

              0 - consensus 1 - multiple sequence alignment 2 - 0 & 1

       --version

              prints the version number

       -h, --help

              prints the usage

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

spoa 1.1.3                                          June 2018                                            SPOA(1)