TreeTime command line usage

TreeTime implements a command line interface (for details, see Command-line API) that allow estimation of time scaled phylogenies, ancestral reconstruction, and analysis of temporal signal in alignments. The command interface is organized as the main command performing time-tree estimation as

treetime --tree tree_file --aln alignment --dates dates.tsv

with other functionalities available as subcommands

treetime {ancestral, clock, homoplasy, mugration, arg, version}

TreeTime can use full alignments in fasta or phylip format or work of VCF files. For each of the different subcommands, we prepared tutorials listed below. These tutorials use example data provided in the github-repository github.com/neherlab/treetime_examples.

• Estimation of time scaled phylogenies
• Ancestral sequence reconstruction using TreeTime
• Estimation of evolutionary rates and tree rerooting
• Inference of transition between discrete characters and ‘mugration’ models
• Analyzing homoplasies and recurrent mutations using TreeTime