---
name: "pxseqgen"
section: "1"
platform: "linux"
package: "phyx"
version: "1.3.2+ds-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pxseqgen"
---

# pxseqgen(1)

sequence simulator under the GTR model

## NAME

pxseqgen - sequence simulator under the GTR model

## SYNOPSIS

**pxseqgen** \[*OPTIONS*\]...

## DESCRIPTION

Basic sequence simulator under the GTR model. This will take fasta, fastq, phylip, and nexus formats from a file or STDIN.

## OPTIONS

- **-t**, **--treef**=*FILE*

  input treefile, STDIN otherwise

- **-l**, **--length**=*INT*

  length of sequences to generate. default is 1000

- **-b**, **--basef**=*Input*

  comma-delimited base freqs in order: A,C,G,T. default is equal

- **-g**, **--gamma**=*INT*

  gamma shape value. default is no rate variation

- **-i**, **--pinvar**=*FLOAT*

  proportion of invariable sites. default is 0.0

- **-r**, **--ratemat**=*Input*

  comma-delimited input values for rate matrix. default is JC69 order: A\<-\>C,A\<-\>G,A\<-\>T,C\<-\>G,C\<-\>T,G\<-\>T

- **-w**, **--aaratemat**=*Input*

  comma-delimited amino acid rate matrix. default is all freqs equal order is ARNDCQEGHILKMFPSTWYV

**-q**, **--aabasefreq**=*Input* AA frequencies, order: ARNDCQEGHILKMFPSTWYV

- **-c**, **--protein**

  run as amino acid

- **-n**, **--nreps**=*INT*

  number of replicates

- **-x**, **--seed**=*INT*

  random number seed, clock otherwise

- **-a**, **--ancestors**

  print the ancestral node sequences. default is no use **-p** for the nodes labels

- **-p**, **--printnodelabels**

  print newick with internal node labels. default is no

- **-m**, **--multimodel**=*Input* specify multiple models across tree

  input is as follows:

- A\<-\>C,A\<-\>G,A\<-\>T,C\<-\>G,C\<-\>T,G\<-\>T,Node#,A\<-\>C,A\<-\>G,A\<-\>T,C\<-\>G,C\<-\>T,G\<-\>T

  EX:.3,.3,.3,.3,.3,1,.3,.3,.2,.5,.4

- **-k**, **--rootseq**=*STRING*

  set root sequence. default is random (from basefreqs)

- **-o**, **--outf**=*FILE*

  output seq file, STOUT otherwise

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

  display this help and exit

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

  display version and exit

- **-C**, **--citation**

  display phyx citation and exit

## CITATION

Brown, Joseph W., Joseph F. Walker, and Stephen A. Smith. 2017. Phyx: phylogenetic tools for unix. Bioinformatics 33(12): 1886-1888. https://doi.org/10.1093/bioinformatics/btx063.

## AUTHOR

Written by Joseph F. Walker, Joseph W. Brown, Stephen A. Smith (blackrim)

## REPORTING BUGS

Report bugs to: \<https://github.com/FePhyFoFum/phyx/issues\> phyx home page: \<https://github.com/FePhyFoFum/phyx\>

## COPYRIGHT

Copyright © 2015-2024 FePhyFoFum License GPLv3