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.