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

# base\_evolve(1)

Produce a synthetic alignment by simulating evolution according to

## NAME

base\_evolve - Produce a synthetic alignment by simulating evolution according to

## DESCRIPTION

Produce a synthetic alignment by simulating evolution according to a phylogenetic model or a phylo-HMM.  Deals with base-substitution only, not indels.  If a multiple tree models are given, then an HMM file must be given showing how to transition between them.

## EXAMPLE

-

  base\_evolve **--nsites** 500 mytree.mod \> simulated.fa

-

  base\_evolve **--nsites** 500 simple-gene.hmm tree1.mod tree2.mod \\ tree3.mod **--features** simulated2.gff **--catmap** simple-gene.cm \\ \> simulated2.fa

## OPTIONS

**--nsites**, **-n** \<nsites\> Generate an alignment with \<nsites\> columns. Default is 1000.

**--msa-format**, **-o** FASTA\|PHYLIP\|MPM\|SS

- Output alignment in specified format.

  Default is FASTA.

**--features**, **-f** \<out.gff\> (for use with a phylo-HMM) Output an annotations file in GFF

-

  reflecting the path through the phylo-HMM.

**--catmap**, **-c** \<map.cm\>

- (for use with **--features**)

  Use specified category map to

-

  define feature names.

**--embed**, **-e** \<alt.mod\>,\<length\> Embed an artificial element of the given length in the alignment, drawing columns from \<alt.mod\>.  A single element is embedded in the exact middle of the generated alignment.  Useful for testing sensitivity of methods for functional element detection.

**--help**, **-h**

-

  Display this help message and exit.