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

# alignments-diff(1)

Align two alignments for comparison.

## NAME

**alignments-diff** - Align two alignments for comparison.

## SYNOPSIS

**alignments-diff** alignment-file1 alignment-file2 \[OPTIONS\]

## DESCRIPTION

Align two alignments for comparison.

## GENERAL OPTIONS:

- **-h**, **–help**

  produce help message

## INPUT OPTIONS:

- **–alphabet** *arg*

  set to \`Codons' to prefer codon alphabets

## OUTPUT OPTIONS:

- **–merge**

  Stack the two alignments into one alignment with duplicate names

- **–dual**

  Write out the two aligned alignments separately

- **–fill** *arg* (=gap)

  blank columns filled with: gap or unknown

- **-d** *arg*, **–differences-file** *arg*

  Filename to store differences in AU format

- **–blocksize** *arg* (=20)

  Width of blocks of same color

- **–classes** *arg* (=1)

  Number of groups for non-matching characters

## 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.