Collections of examples of phylogenetic analysis with TreeTime

There are three different ways of using TreeTime:

1. as a python module as part of python scripts and programs
2. via a set of command-line tools
3. via the webserver at treetime.ch.

The documentation of TreeTime is now hosted on readthedocs:

Command line usage

The general pattern to use TreeTime to infer timetrees via the command line is

treetime --tree mytree.nwk --aln mysequences.fasta --dates metadata.csv

In addition, there are number of subcommands for related tasks. Please see the following pages that explain usage for different cases:

• timetree estimation
• estimation of substitution rates
• ancestral sequence reconstruction
• homoplasy analysis
• discrete traits and mugration models

TreeTime in python scripts

A minimal script to run TreeTime would look something like this

from treetime import TreeTime
from treetime.utils import parse_dates

dates=parse_dates('metadata.csv')
tt=TreeTime(tree='mytree.nwk', aln='mysequences.fasta', dates=dates)
tt.run(root='best')

More detailed examples can be found in the following set of scripts:

• rerooting and timetree inference
• ancestral sequence reconstruction
• relaxed clock models
• an analysis of 2014-2016 Ebola virus sequences