alignment-identity(1)

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>.

AUTHORS
Benjamin Redelings.