alignment-max1

Usage

Overview

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 (=multiply)

sum, wsum, wsum2, multiply

–column-pr arg (=homology)

homology, alignment

-S arg (=1), –sort arg (=1)

Sort partially ordered columns to group similar gaps

-o arg (=-), –out arg (=-)

Output file (defaults to stdout)

-p arg, –out-probabilities arg

Output file for column probabilities, if specified

–debug-graph arg

Filename for debug graph

-V, –verbose

Output more log messages on stderr.

Reporting bugs:

BAli-Phy online help: ⟨http://www.bali-phy.org/docs.php⟩\c .

Please send bug reports to ⟨[email protected]⟩\c .