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

# pxstrec(1)

conduct state reconstruction analyses

## NAME

pxstrec - conduct state reconstruction analyses

## SYNOPSIS

**pxstrec** \[*OPTIONS*\]... *FILES*

## DESCRIPTION

This will conduct state reconstruction analyses.

## OPTIONS

- **-d**, **--dataf**=*FILE*

  input data file

- **-w**, **--datawide**

  data is in wide format so (001 instead of 2)

- **-z**, **--dataz**

  data is in probability format (0,1,0,0)

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

  input tree file

- **-c**, **--conf**=*FILE*

  configuration file

**-n**, **--outstnum**=*FILE* output file for stochastic mapping number

**-a**, **--outstnumany**=*FILE* output file for stochastic mapping number any

**-m**, **--outsttim**=*FILE* output file for stochastic mapping duration

- **-p**, **--periods**=*NUMS*

  comma separated times

- **-l**, **--logf**=*FILE*

  log file, STOUT otherwise

- **-o**, **--outanc**=*FILE*

  output file for ancestral calc

- **-s**, **--silent**

  less verbose output (default: false)

- **-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 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 © 2017-2024 FePhyFoFum License GPLv3