treetime

Infer ancestral sequences maximizing the joint or marginal likelihood

$ treetime ancestral

$ treetime homoplasy

$ treetime clock

$ treetime mugration

treetime [options]

--aln
    Sequence alignment file (FASTA format).

--tree
    Phylogenetic tree file (Newick format).

--dates
    File containing sampling dates for each sequence (CSV or TSV format).

--clock-rate
    Initial estimate of the clock rate.

--reroot
    Reroot the tree. Available methods: 'best', 'midpoint'.

--model
    Specify the GTR model for ancestral state reconstruction.

--outdir
    Specify the output directory.

ancestral
    Reconstruct ancestral sequences.

date-range
    Refine node times conditioned on the given date range.

Treetime is a Python package and command-line tool for inferring ancestral states, time-scaled phylogenies, and evolutionary dynamics from sequence data. It leverages the relationship between phylogenetic trees and temporal information (e.g., sampling dates) to estimate parameters such as substitution rates, root-to-tip regression, and clock models. It is particularly useful for analyzing viral evolution, enabling the reconstruction of viral phylogenies with accurate time scales. Treetime employs efficient algorithms to handle large datasets and complex models, allowing for real-time monitoring of evolutionary processes. The command-line interface `treetime` allows users to perform various analyses including time-tree inference, ancestral state reconstruction, and clock rate estimation. The tool accepts various input formats including FASTA sequence alignments, phylogenetic trees in Newick format, and metadata about the sequences. Its output includes time-scaled trees, ancestral sequences, and parameter estimates that can be used for further analysis and visualization.

The `treetime` tool provides several subcommands such as `ancestral`, `date-range`, and `mugration` each designed for a specific type of analysis. Run `treetime --help` for a complete list of subcommands and their options.

Treetime requires correctly formatted input files. Ensure that the sequence names in the FASTA alignment, tree file, and dates file are consistent. Date file format needs to contain sequence names and corresponding sampling dates in a machine readable format.

iqtree(1), raxml(1)