NAME

alignment-identity - Report statistics on pairwise identity.

SYNOPSIS

alignment-identity [OPTIONS] < sequence-file

DESCRIPTION

Report statistics on pairwise identity.

ALLOWED OPTIONS:

-h, --help

produce help message

--alphabet arg

Specify the alphabet: DNA, RNA, Amino-Acids, Amino-Acids+stop, Triplets, Codons, or Codons+stop.

--with-indels

Calculate percent-identity w/ indels

--seed arg

random seed

--skip arg (=0)

number of tree samples to skip

--max-alignments arg (=1000)

maximum number of alignments to analyze

--cutoff arg (=0.75)

ignore events below this probability

--identity arg (=0.40000000000000002)

Find fraction of sequences that have this level of identity.

--analysis arg

What analysis to do: default, matrix, nmatrix

--strict

require all implied pairs pass the cutoff

REPORTING BUGS:

BAli-Phy online help: http://www.bali-phy.org/docs.php.

Please send bug reports to bali-phy-users@googlegroups.com.