treetime
Treetime is a command line tool specifically designed for evolutionary analysis of molecular sequences. It allows for the inference of temporal and phylogenetic relationships among sequences, commonly used in the study of viruses and bacteria. Treetime provides a wide range of functionalities to perform molecular dating, estimate mutation rates, and reconstruct ancestral sequences. This tool utilizes a Bayesian approach to estimate the phylogenetic tree from sequence alignments, incorporating molecular clock models for accurate time estimation. Treetime also employs maximum likelihood methods to optimize substitution models and assess branch support values. It supports the analysis of large-scale datasets efficiently, and the output is easily interpretable and customizable. Overall, Treetime is a powerful and versatile tool that aids researchers in understanding the evolutionary dynamics and timeline of molecular sequences.
List of commands for treetime:
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treetime:tldr:1c07f treetime: Analyze patterns of recurrent mutations aka homoplasies.$ treetime homoplasytry on your machineexplain this command
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treetime:tldr:2a461 treetime: Estimate molecular clock parameters and reroot the tree.$ treetime clocktry on your machineexplain this command
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treetime:tldr:39f8f treetime: Map discrete character such as host or country to the tree.$ treetime mugrationtry on your machineexplain this command
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treetime:tldr:a805a treetime: Infer ancestral sequences maximizing the joint or marginal likelihood.$ treetime ancestraltry on your machineexplain this command