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

# alignment-cat(1)

Concatenate several alignments (with the same sequence names) end-to-end.

## NAME

**alignment-cat** - Concatenate several alignments (with the same sequence names) end-to-end.

## SYNOPSIS

**alignment-cat** *file1* \[*file2* ...\]

## DESCRIPTION

Concatenate several alignments (with the same sequence names) end-to-end.

## ALL OPTIONS:

- **-h**, **–help**

  Produce help message

- **–output** *arg* (=fasta)

  Which output format: fasta or phylip?

- **-c** *arg*, **–columns** *arg*

  Ranges of columns to keep, like: 1-10,30-

- **-t** *arg*, **–taxa** *arg*

  Taxa to keep, comma-separated

- **-p**, **–pad**

  Add gaps to make sequence lengths identical

- **-r**, **–reverse**

  Reverse the sequences

- **-e**, **–erase-empty-columns**

  Remove columns with no characters (all gaps).

- **–missing** *arg* (=-?)

  What letters are not characters (e.g. gaps)?

- **–strip-gaps**

  Remove all non-character letters from sequences.

- **–reorder-by-tree** *arg*

  Reorder the sequences given a tree

- **–use-root**

  use the root specified in the tree file to reorder

- **–reorder-by-alignment** *arg*

  Reorder the sequences following an alignment

- **–align-by-amino** *arg*

  Arrange nucleotides into codon alignment

## EXAMPLES:

To select columns from an alignment:

-

  ```
  % alignment-cat -c1-10,50-100,600- filename.fasta > result.fasta
  % alignment-cat -c5-250/3 filename.fasta > first_codon_position.fasta
  % alignment-cat -c6-250/3 filename.fasta > second_codon_position.fasta
  ```

To concatenate two or more alignments:

-

  ```
  % alignment-cat filename1.fasta filename2.fasta > all.fasta
  ```

## 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.