---
name: "msa_diff"
section: "1"
platform: "linux"
package: "phast"
version: "1.7+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/msa_diff"
---

# msa\_diff(1)

Compare two multiple alignments and report differences.

## NAME

msa\_diff - Compare two multiple alignments and report differences.

## DESCRIPTION

Compare two multiple alignments and report differences.

## OPTIONS

**--format1**, **-i** FASTA\|SS\|PHYLIP\|MPM\|MAF

-

  Format of first alignment (default is to guess format from file contents).

**--format2**, **-j** FASTA\|SS\|PHYLIP\|MPM\|MAF Format of second alignment (default is to guess format from file contents).

**--alphabet**, **-a** \<alphabet\_string\> Use given string for alphabet. Can be used to accommodate

-

  nonstandard characters (e.g., 'b' for any base or '^' for insertion gaps, '.' for deletion gaps).

**--ignore-base-id**, **-b** Ignore identity of bases; consider all alphabetical characters equivalent (e.g., A, C, G, T, N, X, b).

**--ignore-gap-type**, **-g**

-

  Ignore type of gap; consider '-', '^', and '.' all equivalent.

**--help**, **-h** Display this help message and exit.