---
name: "chainsaw"
section: "1"
platform: "linux"
package: "prime-phylo"
version: "1.0.11-13+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/chainsaw"
---

# chainsaw(1)

Cut a gene tree based on a reconciliation

## NAME

chainsaw - Cut a gene tree based on a reconciliation

## SYNOPSIS

**chainsaw** \[*OPTIONS*\] *reconciled-gene-tree*  *species-tree*

## DESCRIPTION

*reconciled-gene-tree is the filename of the file containing trees in PRIME* format. Notice that the node id is optional and if left out all species  nodeswill be used recursively.

*species-tree is the species tree*

## OPTIONS

- **--help**

  Display help (this text).

- **-V**, **--version**

  Print version and exit

- **-g**, **--guest-tree-format** **primeOrHybrid\|inputxml**

  The input format. Default is primeOrHybrid

- **-h**, **--host-tree-format** **primeOrHybrid\|inputxml**

  The input format of the host tree. Default is primeOrHybrid

- **-x**, **--node-name=STRING**

  A named species node to cut at

- **-i**, **--node-id=INT**

  The numerical id of a species node to cut at

## EXIT STATUS

- **0**

  Successful program execution.

- **1**

  Some error occurred

## URL

- The prime-phylo home page: http://prime.sbc.su.se

  ## SEE ALSO

[**primeDTLSR**(1)](/primeDTLSR/1.md), [**primeDLRS**(1)](/primeDLRS/1.md), [**primeGEM**(1)](/primeGEM/1.md), [**showtree**(1)](/showtree/1.md), [**reconcile**(1)](/reconcile/1.md), [**reroot**(1)](/reroot/1.md), [**tree2leafnames**(1)](/tree2leafnames/1.md), [**treesize**(1)](/treesize/1.md)