NAME¶

temporal_signal - Calculates the root-to-tip regression and quantifies the 'clock-i-ness' of a tree

SYNOPSIS¶

temporal_signal [-h] --tree TREE --dates DATES [--aln ALN] [--infer_gtr] [--reroot] [--plot] [--verbose VERBOSE]

DESCRIPTION¶

Calculates the root-to-tip regression and quantifies the 'clock-i-ness' of the tree. It will optionally reroot the tree to maximize the clock-like signal and recalculate branch length.

OPTIONS¶

-h, --help

show this help message and exit

--tree TREE

newick file with tree

--dates DATES

csv with dates for nodes with 'node_name, date' where date is float (as in 2012.15)

--aln ALN

fasta file with input sequences

--infer_gtr

infer substitution model

--reroot

reroot the tree to maximize the correlation of root-totip distance with sampling time

--plot

--verbose VERBOSE

verbosity of output 0-6

AUTHOR¶

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.