---
name: "phast"
section: "1"
platform: "linux"
package: "phast"
version: "1.7+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/phast"
---

# phast(1)

phylogenetic analysis with space/time models

## NAME

phast - phylogenetic analysis with space/time models

## DESCRIPTION

The PHAST package contains the following programs:

- all\_dists

  hmm\_view        phastBias

- base\_evolve

  indelFit        phastCons

- chooseLines

  indelHistory    phastMotif

- clean\_genes

  maf\_parse       phastOdds

- consEntropy

  makeHKY         phyloBoot

- convert\_coords

  modFreqs        phyloFit

- display\_rate\_matrix

  msa\_diff        phyloP

- dless

  msa\_split       prequel

- dlessP

  msa\_view        refeature

- draw\_tree

  pbsDecode       stringiphy

- eval\_predictions

  pbsEncode       test

- exoniphy

  pbsScoreMatrix  tree\_doctor

- hmm\_train

  pbsTrain        treeGen

- hmm\_tweak

  phast

-

  For help, type the program's name followed by **-h** in your command line window.