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.

       --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>.

AUTHORS

       Benjamin Redelings.

                                             Feb 2018                      alignment-consensus(1)