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

# trees-consensus(1)

Find consensus trees and supported splits.

## NAME

**trees-consensus** - Find consensus trees and supported splits.

## SYNOPSIS

**trees-consensus** \[OPTIONS\] *sampled-trees* \[*sampled-trees* ... *sampled-trees*\]

## DESCRIPTION

Find consensus trees and supported splits.

## INPUT OPTIONS:

- **-h**, **–help**

  Produce help message.

- **-V**, **–verbose**

  Output more log messages on stderr.

- **-s** *arg* (=10%), **–skip** *arg* (=10%)

  Number of trees 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.

- **-i** *arg*, **–ignore** *arg*

  Comma-separated list of taxa to ignore.

## REPORTING OPTIONS:

- **–map-trees** *arg* (=1)

  Only report the top *arg* trees per file.

- **–min-support** *arg* (=0.25)

  Minimum threshold PP for splits.

- **–report** *arg*

  Write supported partitions to file *arg*.

- **–map-tree** *arg*

  Write out the map tree to file *arg*.

- **–consensus** *arg*

  Write out consensus trees.

- **–greedy-consensus** *arg*

  Write out greedy consensus trees.

- **–extended-consensus-L** *arg*

  Write out extended consensus trees + lengths.

- **–extended-consensus** *arg*

  Write out extended consensus trees.

- **–support-levels** *arg*

  Write #branches versus LOD to file *arg*.

- **–extended-support-levels** *arg*

  Write #sub-branches versus LOD to file *arg*.

## SEARCH OPTIONS:

- **–sub-partitions**

  Search for partial splits.

- **–depth** *arg* (=1)

  Depth at which to look for partial splits.

- **–rooting** *arg* (=0.9)

  Threshold in search for partial splits.

- **–odds-ratio** *arg* (=1.5)

  Report partial-splits only if removing taxa improves the odds by at least this ratio.

## EXAMPLES:

Compute the majority consensus tree, skipping the first 10% of trees:

-

  ```
  % trees-consensus newick.trees > c50.tree
  % trees-consensus newick.trees --skip=10% > c50.tree
  ```

Skip the first 100 trees:

-

  ```
  % trees-consensus newick.trees --skip=100 > c50.tree
  ```

Skip the first 20% of trees and take every 10th tree thereafter:

-

  ```
  % trees-consensus newick.trees --skip=20% -x10 > c50.tree
  ```

Compute the 50% (majority) and 80% consensus trees:

-

  ```
  % trees-consensus newick.trees --consensus=0.5:c50.tree,0.8:c80.tree
  % trees-consensus newick.trees --consensus=0.5,0.8:c80.tree > c50.tree
  ```

Compute the MAP tree and write a summary of supported partitions:

-

  ```
  % trees-consensus --map-tree=MAP.tree --report=partitions.txt
  ```

Compute the MAP tree and write it to the standard output:

-

  ```
  % trees-consensus --map-tree=- --report=partitions.txt
  ```

## 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.