pxlog(1) · carta

Usage

pxlog [OPTIONS] ...

Overview

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.

Releases

3 releases since Debian 10 (Buster); the text changed 2 times.

10
12
13

--citation since Debian 12 (Bookworm); --columns since Debian 12 (Bookworm); --delete since Debian 12 (Bookworm); --keep since Debian 12 (Bookworm); --summarize since Debian 12 (Bookworm); -C since Debian 12 (Bookworm); -c since Debian 12 (Bookworm); -d since Debian 12 (Bookworm); -k since Debian 12 (Bookworm); -s since Debian 12 (Bookworm).

--rand until Debian 10 (Buster); --seed until Debian 10 (Buster); -r until Debian 10 (Buster); -x until Debian 10 (Buster).