chainsaw(1)

Usage

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

Overview

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

Releases

Unchanged in 6 releases since Debian 8 (Jessie).

8–13

Referred to by

reroot(1) Compute a (new) root for the tree. primeGEM(1) Guest-in-host tree reconciliation tool showtree(1) View and/or convert phylogenetic trees in the terminal. treesize(1) Count the leaves of trees. primeDLRS(1) Guest-in-host tree reconciliation tool primeGSRf(1) Guest-in-host tree reconciliation tool reconcile(1) This program outputs the reconciliation that minimizes the number of duplications primeDTLSR(1) Guest-in-host tree inference tool mcmc_analysis(1) Analysis of the MCMC tree2leafnames(1) List the leaves of a tree