treetime

Infer ancestral sequences

$ treetime ancestral

$ treetime homoplasy

$ treetime clock

$ treetime mugration

treetime COMMAND [OPTIONS]

treetime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies. It is used in phylogenetic analysis to understand evolutionary relationships and timing of divergence events.
The tool can reconstruct ancestral sequences, detect homoplasies (convergent evolution), estimate mutation rates, and map geographic or host information onto phylogenetic trees.

ancestral

Infer ancestral sequences maximizing likelihood

Analyze patterns of recurrent mutations

Estimate molecular clock parameters and reroot tree

Map discrete characters (host, country) to tree

Requires phylogenetic tree and sequence alignment inputs. Computationally intensive for large datasets. Results depend on model assumptions.

treetime was developed for phylogenetic analysis in molecular epidemiology and evolutionary biology, providing tools for understanding pathogen evolution and spread.

iqtree(1), raxml(1)