NAME

       alignment-max - Construct a posterior decoding alignment to summarize an alignment sample.

SYNOPSIS

       alignment-max [OPTIONS] < alignments-file

DESCRIPTION

       Construct a posterior decoding 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.

       -s arg (=0), --skip arg (=0)
              Number of alignment samples to skip

       -m arg (=1000), --max-alignments arg (=1000)
              Maximum number of alignments to analyze

       --analysis arg (=wsum)
              sum, wsum, wsum2, multiply

       -o arg (=-), --out arg (=-)
              Output file (defaults to stdout)

       -p arg, --out-probabilities arg
              Output file for column probabilities, if specified

       -V, --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-max(1)