---
name: "alter-sequence-alignment"
section: "1"
platform: "linux"
package: "alter-sequence-alignment"
version: "1.3.4-8"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/alter-sequence-alignment"
---

# alter-sequence-alignment(1)

genomic sequences ALignment Transformation EnviRonment

## NAME

alter-sequence-alignment - genomic sequences ALignment Transformation EnviRonment

## SYNOPSIS

**alter-sequence-alignment** *\[option\] \[sequence\]*

## DESCRIPTION

 ALTER (ALignment Transformation EnviRonment) is a tool to transform\
  between multiple sequence alignment formats. ALTER focuses on the\
  specifications of mainstream alignment and analysis programs rather than\
  on the conversion among more or less specific formats.

## OPTIONS

- **-c** (**--collapse**)

  Collapse sequences to haplotypes.

- **-cg** (**--collapseGaps**)

  Treat gaps as missing data when collapsing.

- **-cl** (**--collapseLimit**) N

  Connection limit (sequences differing at \<= l sites will be collapsed) (default is l=0).

- **-cm** (**--collapseMissing**)

  Count missing data as differences when collapsing.

- **-i** (**--input**) FILE

  Input file.

- **-ia** (**--inputAutodetect**)

  Autodetect format (other input options are omitted).

- **-if** (**--inputFormat**) VAL

  Input format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR).

- **-io** (**--inputOS**) VAL

  Input operating system (Linux, MacOS or Windows)

- **-ip** (**--inputProgram**) VAL

  Input program (Clustal, MAFFT, MUSCLE, PROBCONS or TCoffee).

- **-o** (**--output**) FILE

  Output file.

- **-of** (**--outputFormat**) VAL

  Output format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR).

- **-ol** (**--outputLowerCase**)

  Lowe case output.

- **-om** (**--outputMatch**)

  Output match characters.

- **-on** (**--outputResidueNumbers**)

  Output residue numbers (only ALN format).

- **-oo** (**--outputOS**) VAL

  Output operating system (Linux, MacOS or Windows).

- **-op** (**--outputProgram**) VAL

  Output program (jModelTest, MrBayes, PAML, PAUP, PhyML, ProtTest, RAxML, TCS, CodABC, BioEdit, MEGA, dnaSP, Se-Al, Mesquite, SplitsTree, Clustal , MAFFT, MUSCLE, PROBCONS, TCoffee, Gblocks, SeaView, trimAl or GENERAL)

- **-os** (**--outputSequential**)

  Sequential output (only NEXUS and PHYLIP formats).