pxstrec1

Usage

Overview

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.