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

# alignment-chop-internal(1)

Remove ancestral sequences from an alignment.

## NAME

**alignment-chop-internal** - Remove ancestral sequences from an alignment.

## SYNOPSIS

**alignment-chop-internal** \[OPTIONS\] \< *alignments-file*

## DESCRIPTION

Remove ancestral sequences from an alignment.

## ALLOWED OPTIONS:

- **-h**, **–help**

  produce help message

- **–align** *arg*

  file with sequences and initial alignment

- **–alphabet** *arg*

  set to \`Codons' to prefer codon alphabets

- **–tree** *arg*

  file with tree that specifies leaves to keep

- **-N** *arg*, **–nleaves** *arg*

  number of sequences to keep

## 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.