pxlog(1)

manual page for pxlog 1.3

Section 1 phyx bookworm source

Description

PXLOG

NAME

pxlog - manual page for pxlog 1.3

SYNOPSIS

pxlog [OPTIONS]...

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).

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

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 Joseph W. Brown

REPORTING BUGS

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