---
name: "mlagan"
section: "1"
platform: "linux"
package: "lagan"
version: "2.0-10"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/mlagan"
---

# mlagan(1)

highly parametrizable pairwise global aligner

## NAME

mlagan - highly parametrizable pairwise global aligner

## SYNOPSIS

mlagan seqfile\_1 seqfile\_2 \[... seqfile\_63\] \[-parameters\]

## DESCRIPTION

Lagan takes local alignments generated by CHAOS as anchors, and limits the search area of the Needleman-Wunsch algorithm around these anchors.

Multi-LAGAN is a generalization of the pairwise algorithm to multiple sequence alignment.  M-LAGAN performs progressive pairwise alignments, guided by a user-specified phylogenetic tree. Alignments are aligned to other alignments using the sum-of-pairs metric.

## OPTIONS

- **-nested** : runs improvement in a nested fashion

  - **-postir** : incorporates the final improvement phase

  - **-lazy** : uses lazy mode

  - **-translate** : use translated anchors

  - **-fastreject** : use fast rejection (tuned for human/mouse or closer)

  - **-verbose** : give debug output

  - **-tree** "(...)" : runs with given phylogenetic tree

  - **-out** "filename": outputs to filename

  - **-nucmatrixfile** "filename": uses given substitution matrix instead of *$LAGAN\_DIR/nucmatrix.txt*

  - **-version** : prints version info

  **-nested** : runs improvement in a nested fashion

- **-postir** : incorporates the final improvement phase

  - **-lazy** : uses lazy mode

  - **-translate** : use translated anchors

  - **-fastreject** : use fast rejection (tuned for human/mouse or closer)

  - **-verbose** : give debug output

  - **-tree** "(...)" : runs with given phylogenetic tree

  - **-out** "filename": outputs to filename

  - **-nucmatrixfile** "filename": uses given substitution matrix instead of *$LAGAN\_DIR/nucmatrix.txt*

  - **-version** : prints version info

  ## ENVIRONMENT

The LAGAN\_DIR variable specifies the location of the nucmatrix file. It defaults to /usr/lib/lagan, where Debian also place that file.