---
name: "alignment-max"
section: "1"
platform: "linux"
package: "bali-phy"
version: "4.0-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/alignment-max"
---

# alignment-max(1)

Construct a posterior decoding alignment to summarize an alignment sample.

## 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* (=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 ⟨bali-phy-users@googlegroups.com⟩\\c .

## AUTHORS

Benjamin Redelings.