bionic (1) temporal_signal.1.gz

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.