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

# trees-bootstrap(1)

Compare support for partitions between different files.

## NAME

**trees-bootstrap** - Compare support for partitions between different files.

## SYNOPSIS

**trees-bootstrap** *file1* \[*file2* ... \] –predicates *predicate file* \[OPTIONS\]

## DESCRIPTION

Compare support for partitions between different files.

## INPUT OPTIONS:

- **-h**, **–help**

  Produce help message.

- **-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*, **–subsample** *arg*

  Factor by which to sub-sample.

- **–predicates** *arg*

  Predicates to examine.

- **–min-support** *arg* (=0.1)

  Minimum value of predicates to consider interesting..

- **-V**, **–verbose**

  Output more log messages on stderr.

## BLOCK BOOTSTRAP OPTIONS:

- **–bootstrap**

  Do block bootstrapping to get a CI on the posterior probabilities.

- **–samples** *arg* (=10000)

  Number of bootstrap samples.

- **–pseudocount** *arg* (=1)

  Extra 0/1 to add to bootstrap samples.

- **–blocksize** *arg*

  Block size to use in block boostrap.

- **–seed** *arg*

  Random seed.

## REPORTING OPTIONS:

- **–separation** *arg* (=0)

  Only report trees/partitions if they differ by this many LODs

- **–confidence** *arg* (=0.95)

  Width of confidence intervals

- **–LOD-table** *arg*

  Write the partitions LOD10’s to a file.

## 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.