pxlog - MCMC log file manipulator

Author

       Written by 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 © 2016-2024 FePhyFoFum License GPLv3

pxlog 1.3.1                                         June 2024                                           PXLOG(1)

Description

       MCMC  log  file  manipulator.  Can combine and resample parameters or trees across files.  Log files need
       not contain the same number of samples.  Input files may be  indicated  using  wildcards  e.g.  '*.trees'
       Parameter log files are expected to be whitespace delimited.  *NOTE* All values are in terms of number of
       SAMPLES (NOT generations).

Name

       pxlog - MCMC log file manipulator

Options

-p, --parmf=FILE
              input parameter log file(s)

       -t, --treef=FILE
              input tree log file(s)

       -b, --burnin=INT
              number of samples to exclude at the beginning of a file

       -n, --thin=INT
              interval of resampling

       -i, --info
              calculate log file attributes and exit

       -s, --summarize
              summary statistics of samples (parameter logs only)

       -c, --columns
              print out column names (parameter logs only)

       -d, --delete=CSL
              delete parm columns by 1-index sep by commas (NO SPACES!)

       -k, --keep=CSL
              keep only parm columns by 1-index sep by commas (NO SPACES!)

       -v, --verbose
              make the output more verbose

       -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>