---
name: "phyutility"
section: "1"
platform: "linux"
package: "phyutility"
version: "2.7.3+dfsg-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/phyutility"
---

# phyutility(1)

tools for manipulating sequences and phylogenies

## NAME

phyutility - tools for manipulating sequences and phylogenies

## SYNOPSIS

**phyutility** *\<command\>* *\<options\>*

## DESCRIPTION

Phyutility is a command line program that performs simple analyses or modifications on both trees and data matrices.

## OPTIONS

To get help on a specific command use option **-h** \<command\>

### COMMANDS

**for trees:**

- consensus

   Calculate consensus trees. Use like -con -t \<threshold\> -in \<infile\> -out \<outfile\>.

- convert

   Convert tree files. Use like -vert -in \<infile\> -out \<outfile\>.

- leafstab

   Leaf stability index calculation. Use like -ls -in \<infile\>.

- linmove

   Lineage movement calculation. Use like -lm -names \<tip names\> -tree \<consensus\> -in \<infile\> -out \<outfile\>.

- prune

   Prune lineages. Use like -pr -names \<tip names\> -in \<infile\> -out \<outfile\>.

- reroot

   Reroot trees. Use like -rr -names \<tip names\> -in \<infile\> -out \<outfile\>.

- thin

   Thin trees. Use like -tt # -in \<infile\> -out \<outfile\>.

- treesupp

   Support for a set of trees. Use like -ts -tree \<tree\> -in \<infile\> -out \<outfile\>.

- **for seqs:**

  - clean

   Trim seqs based on threshold. Use like -clean # -in \<infile\> -out \<outfile\> -aa \<to force aa\>.

- concat

   Concatenate alignments. Use like -concat -in \<infiles\> -out \<outfile\> -aa \<to force aa\>.

- ncbiget

   Fetch seqs from NCBI. For options run phyutility -h ncbiget.

- ncbisearch

   Search NCBI. For options run phyutility -h ncbisearch.

- parse

   Parse genbank results. For options run phyutility -h parse.

## EXAMPLE

- phyutility -con -t 0.5 -in testall.tre -out test.con

  Consensus the set of trees in testall.tre collapsing branches with less than 0.5 frequency.

- phyutility -vert -in test.tre -out testvert.nex

  Convert the tree file from newick in test.tre into nexus in testvert.nex.

- phyutility -concat -in test.aln test2.aln -out testall.nex

  Concatenate 2 alignment files into nexus in testall.nex.

## SEE ALSO

See documentation at https://github.com/blackrim/phyutility/blob/master/manual.pdf?raw=true for more information.

## AUTHOR

Stephen A. Smith http://www.blackrim.org eebsmith@umich.edu