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

# trees-distances(1)

Compute autocorrelations or other functions of tree distances.

## NAME

**trees-distances** - Compute autocorrelations or other functions of tree distances.

## SYNOPSIS

**trees-distances** *analysis* trees-file1 \[trees-file2 ...\]

## DESCRIPTION

Compute autocorrelations or other functions of tree distances.

## INPUT OPTIONS:

- **-h**, **–help**

  produce help message

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

  number of tree samples to skip

- **-u** *arg*, **–until** *arg*

  Read until this number of trees.

- **-m** *arg*, **–max** *arg*

  Thin tree samples down to this number of trees.

- **-x** *arg* (=1), **–subsample** *arg* (=1)

  factor by which to subsample

- **-V**, **–verbose**

  Output more log messages on stderr.

## ANALYSIS OPTIONS:

- **–analysis** *arg* (=matrix)

  Analysis: matrix, autocorrelation, diameter, compare, closest, convergence, converged.

- **–metric** *arg* (=topology)

  Tree distance: topology, branch, internal-branch.

- **–remove-duplicates**

  \[matrix\]: disallow zero distances between points.

- **–max-lag** *arg*

  \[autocorrelation\]: max lag to consider.

- **–CI** *arg* (=0.95)

  Confidence interval size.

- **–converged** *arg* (=0.05)

  Comma-separated quantiles of distance required for converged? (smaller is more strict).

- **–mean**

  Show mean and standard deviation

- **–median**

  Show median and confidence interval

- **–minmax**

  Show minimum and maximum distances

- **–leaves-only**

  Show minimum and maximum distances

- **–topology-only**

  Show minimum and maximum distances

- **–jitter** *arg*

  Amount of noise to add to distances

## 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.