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

# alignment-distances(1)

Compute distances between alignments.

## NAME

**alignment-distances** - Compute distances between alignments.

## SYNOPSIS

**alignment-distances** *analysis* alignments-file1 \[alignments-file2 ...\]

## DESCRIPTION

Compute distances between alignments.

## INPUT OPTIONS:

- **-h**, **–help**

  Produce help message

- **-s** *arg* (=0), **–skip** *arg* (=0)

  Number of alignment samples to skip.

- **-m** *arg* (=1000), **–max** *arg* (=1000)

  Maximum number of alignments to analyze.

- **-V**, **–verbose**

  Output more log messages on stderr.

- **–alphabet** *arg*

  Specify the alphabet: DNA, RNA, Amino-Acids, Amino-Acids+stop, Triplets, Codons, or Codons+stop.

## ANALYSIS OPTIONS:

- **–distances** *arg*

  (=splits:splits2:nonrecall:inaccuracy) Colon-separated list of distances.

- **–analysis** *arg*

  Analysis: score, AxA, NxN, compare, median, distances

- **–CI** *arg* (=0.94999999999999996)

  Confidence interval size.

- **–mean**

  Show mean and standard deviation

- **–median**

  Show median and confidence interval

- **–minmax**

  Show minimum and maximum distances

## EXAMPLES:

Compute distances from true.fasta to each in As.fasta:

-

  ```
  % alignment-distances score true.fasta As.fasta
  ```

Compute distance matrix between all pairs of alignments in all files:

-

  ```
  % alignment-distances AxA file1.fasta ... fileN.fasta
  ```

Compute all NxN pairwise alignment accuracies, averaged over As:

-

  ```
  % alignment-distances NxN true.fasta As.fasta
  ```

Find alignment with smallest average distance to other alignments:

-

  ```
  % alignment-distances median As.fasta A.fasta
  ```

Compare the distances with-in and between the two groups:

-

  ```
  % alignment-distances compare A-dist1.fasta A-dist2.fasta
  ```

Report distribution of average distance to other alignments:

-

  ```
  % alignment-distances distances As.fasta A.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.