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