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

# alignment-gild(1)

Annotate each residue in the alignment according to the probability that it should align to the hypothetical root character in its column.

## NAME

**alignment-gild** - Annotate each residue in the alignment according to the probability that it should align to the hypothetical root character in its column.

## SYNOPSIS

**alignment-gild** alignment-file tree-file alignments-file \[alignments-file\] \[OPTIONS\]

## DESCRIPTION

Annotate each residue in the alignment according to the probability that it should align to the hypothetical root character in its column.

## ALLOWED OPTIONS:

- **-h**, **–help**

  produce help message

- **–align** *arg*

  file with alignment to annotate

- **–tree** *arg*

  file with tree

- **–find-root**

  estimate the root position from branch lengths

- **–alphabet** *arg*

  set to \`Codons' to prefer codon alphabets

- **–skip** *arg* (=0)

  number of alignment samples to skip

- **–max-alignments** *arg* (=1000)

  maximum number of alignments to analyze

- **-V**, **–verbose**

  Output more log messages on stderr.

## 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.