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

# alignment-indices(1)

Show the alignment in terms of the index of each character in its sequence.

## NAME

**alignment-indices** - Show the alignment in terms of the index of each character in its sequence.

## SYNOPSIS

**alignment-indices** *alignment-file* \[OPTIONS\]

## DESCRIPTION

Show the alignment in terms of the index of each character in its sequence.

## ALLOWED OPTIONS:

- **-h**, **–help**

  produce help message

- **–align** *arg*

  file with sequences and initial alignment

- **–alphabet** *arg*

  set to \`Codons' to prefer codon alphabets

- **-c** *arg*, **–columns** *arg*

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

- **–invariant** *arg*

  print only sites where this site and *arg* neighbors are invariant.

- **–differences** *arg*

  how many sequences may differ from the majority?

- **–avoid-gaps** *arg* (=3)

  How far from a gap must a column be to be invariant?

- **–min-constraints** *arg*

  Minimum # of constraints per column for a constraint to be emitted

## 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.