pxbdsim - birth-death tree simulator

Author

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

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.

Copyright

       Copyright © 2013-2024 FePhyFoFum License GPLv3

pxbdsim 1.3.1                                       June 2024                                         PXBDSIM(1)

Description

       Birth-death tree simulator.

Name

       pxbdsim - birth-death tree simulator

Options

-e, --extant=INT
              number of extant species, alt to time

       -t, --time=DOUBLE
              timespan of simulation (age of root), alt to extant

       -b, --birth=DOUBLE
              birth rate, default=1

       -d, --death=DOUBLE
              death rate, default=0

       -n, --nreps=INT
              number of replicates, default=1

       -s, --showextinct
              show lineages that went extinct, default=false

       -x, --seed=INT
              random number seed, clock otherwise

       -v, --verbose
              print per-tree simulation summary (to cerr)

       -o, --outf=FILE
              output file, STOUT otherwise

       -h, --help
              display this help and exit

       -V, --version
              display version and exit

       -C, --citation
              display phyx citation and exit

Reporting Bugs

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