NAME

alignment-consensus -- Construct a consensus alignment to summarize an alignment sample.

SYNOPSIS

alignment-consensus [OPTIONS] < alignments-file

DESCRIPTION

Construct a consensus alignment to summarize an alignment sample.

ALLOWED OPTIONS:

-h, --help
produce help message
--alphabet arg
Specify the alphabet: DNA, RNA, Amino-Acids, Amino-Acids+stop, Triplets, Codons, or Codons+stop.
--seed arg
random seed
--skip arg (=0)
number of tree samples to skip
--max-alignments arg (=1000)
maximum number of alignments to analyze
--strict arg
ignore events below this probability
--cutoff arg
ignore events below this probability
--uncertainty arg
file-name for AU uncertainty vs level
--verbose
Output more log messages on stderr.

REPORTING BUGS:

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

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