.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH PXLOG "1" "July 2021" "pxlog 1.3" "User Commands"
.SH NAME
pxlog \- manual page for pxlog 1.3
.SH SYNOPSIS
.B pxlog
[\fI\,OPTIONS\/\fR]...
.SH 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).
.SH OPTIONS
.TP
\fB\-p\fR, \fB\-\-parmf\fR=\fI\,FILE\/\fR
input parameter log file(s)
.TP
\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
input tree log file(s)
.TP
\fB\-b\fR, \fB\-\-burnin\fR=\fI\,INT\/\fR
number of samples to exclude at the beginning of a file
.TP
\fB\-n\fR, \fB\-\-thin\fR=\fI\,INT\/\fR
interval of resampling
.TP
\fB\-i\fR, \fB\-\-info\fR
calculate log file attributes and exit
.TP
\fB\-s\fR, \fB\-\-summarize\fR
summary statistics of samples (parameter logs only)
.TP
\fB\-c\fR, \fB\-\-columns\fR
print out column names (parameter logs only)
.TP
\fB\-d\fR, \fB\-\-delete\fR=\fI\,CSL\/\fR
delete parm columns by 1\-index sep by commas (NO SPACES!)
.TP
\fB\-k\fR, \fB\-\-keep\fR=\fI\,CSL\/\fR
keep only parm columns by 1\-index sep by commas (NO SPACES!)
.TP
\fB\-v\fR, \fB\-\-verbose\fR
make the output more verbose
.TP
\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
output file, STOUT otherwise
.TP
\fB\-h\fR, \fB\-\-help\fR
display this help and exit
.TP
\fB\-V\fR, \fB\-\-version\fR
display version and exit
.TP
\fB\-C\fR, \fB\-\-citation\fR
display phyx citation and exit
.SH 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.
.SH AUTHOR
Written by Joseph W. Brown
.SH "REPORTING BUGS"
Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
phyx home page: <https://github.com/FePhyFoFum/phyx>
.SH COPYRIGHT
Copyright \(co 2016\-2021 FePhyFoFum
License GPLv3