TreeTime command examples (with examples)

1: Infer ancestral sequences maximizing the joint or marginal likelihood

Code:

treetime ancestral

Motivation: One common task in phylogenetics is to infer the ancestral sequences of a given set of DNA or protein sequences. This can be useful to understand the evolutionary history and functional properties of the sequences. TreeTime provides a convenient command to infer ancestral sequences using the joint or marginal likelihood.

Explanation: The treetime ancestral command runs TreeTime’s ancestral sequence reconstruction algorithm. By default, it uses the joint (maximum likelihood) method to infer ancestral sequences. This method considers the entire phylogenetic tree and the available sequence data to estimate the most likely ancestral sequences.

Example Output:

Ancestral sequences inferred successfully.
Ancestral sequences saved in 'ancestral_sequences.fasta'.

2: Analyze patterns of recurrent mutations aka homoplasies

Code:

treetime homoplasy

Motivation: Understanding the occurrence and distribution of recurrent mutations, also known as homoplasies, is crucial in studying the evolution of certain traits or characteristics in a phylogenetic tree. Analyzing homoplasies can provide insights into the underlying evolutionary mechanisms, such as convergent evolution or genetic convergence.

Explanation: The treetime homoplasy command allows TreeTime to analyze the patterns of recurrent mutations in a given phylogenetic tree. By identifying homoplasies, one can gain insights into the evolutionary dynamics and selective pressures acting on specific genetic loci.

Example Output:

Homoplasies analyzed successfully.
Homoplasies summary saved in 'homoplasy_report.txt'.

3: Estimate molecular clock parameters and reroot the tree

Code:

treetime clock

Motivation: The molecular clock hypothesis assumes that the rate of evolutionary change in DNA or protein sequences is relatively constant over time. Estimating molecular clock parameters, such as the substitution rate, can provide insights into the timing and tempo of evolutionary events. Rerooting the phylogenetic tree based on these estimates can improve the accuracy of ancestral sequence inference.

Explanation: The treetime clock command allows TreeTime to estimate molecular clock parameters and reroot the phylogenetic tree accordingly. It uses maximum likelihood estimation to infer the substitution rate, which is then used to reconstruct the tree with the new root position.

Example Output:

Molecular clock parameters estimated successfully.
Phylogenetic tree rerooted based on the estimated parameters.
Rerooted tree saved in 'rerooted_tree.nwk'.

4: Map discrete character such as host or country to the tree

Code:

treetime mugration

Motivation: In many biological studies, it is essential to analyze the association between genetic data and discrete character traits such as geographic location or host species. Mapping these traits onto the phylogenetic tree can help identify patterns of lineage movement, transmission dynamics, or host shifts.

Explanation: The treetime mugration command allows TreeTime to map discrete character traits to the phylogenetic tree. By providing a file containing the trait values for each sequence, TreeTime can infer and visualize these traits on the tree, facilitating the interpretation of the data.

Example Output:

Discrete character traits mapped successfully.
Mapped tree with discrete character annotations saved in 'mapped_tree.nwk'.

In this article, we have explored different use cases of the TreeTime command. From inferring ancestral sequences to analyzing homoplasies, estimating molecular clock parameters, and mapping discrete character traits, TreeTime provides a versatile toolkit for phylogenetic analysis. By following the provided code examples and understanding the motivations, explanations, and example outputs for each use case, researchers can leverage TreeTime’s functionalities to gain insights into evolutionary dynamics and improve the interpretation of genetic data.