TreeTime is a free and open-source software package for inferring molecular-clock phylogenies and ancestral sequence reconstruction. It provides a suite of tools and algorithms for analyzing sequence data and reconstructing the evolutionary history of biological organisms.
Molecular-clock phylogenies are used to estimate the timing of evolutionary events by assuming that genetic changes accumulate at a constant rate over time. Ancestral sequence reconstruction is the process of inferring the most likely ancestral sequences of biological molecules, such as DNA or proteins, at various points in the evolutionary history of a group of organisms.
TreeTime provides several routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies, including maximum-likelihood and Bayesian methods. The tool also supports the use of multiple sequence alignments and can handle large datasets with thousands of sequences.
TreeTime is written in Python and is designed to be easy to use and flexible. It provides a command-line interface as well as a Python API, making it easy to integrate into existing workflows and pipelines. The tool also provides extensive documentation and tutorials to help users get started and learn more about the different features and capabilities of the software.
treetime Command Examples
1. Infer ancestral sequences maximizing the joint or marginal likelihood:
# treetime ancestral
2. Analyze patterns of recurrent mutations aka homoplasies:
# treetime homoplasy
3. Estimate molecular clock parameters and reroot the tree:
# treetime clock
4. Map discrete character such as host or country to the tree:
# treetime mugration
Summary
Overall, TreeTime is a powerful and versatile tool for ancestral sequence reconstruction and molecular-clock phylogenetics. Its ability to handle large datasets and support multiple methods and algorithms makes it a valuable tool for researchers and scientists working in the field of molecular evolution and phylogenetics.