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Updated: Apr 4, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
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markophylo: Markov chain analysis on phylogenetic trees.
Utkarsh J Dang1, G Brian Golding1
1Department of Biology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
Bioinformatics (Oxford, England)
|September 13, 2015
Summary
Introducing markophylo, a fast R package for inferring evolutionary rates of discrete characters on phylogenetic trees. It uses maximum-likelihood models and Markov chains for efficient phylogenetic analysis.
Area of Science:
- Phylogenetics and evolutionary biology
- Computational biology and bioinformatics
Background:
- Continuous-time Markov chain models are standard for analyzing discrete character data on phylogenetic trees.
- Biologically realistic models incorporating site rate variation and branch-specific rates are increasingly used.
Purpose of the Study:
- To introduce markophylo, a flexible and efficient R package for inferring evolutionary rates of discrete characters.
- To provide a probabilistic framework for phylogenetic analysis of discrete traits.
Main Methods:
- The markophylo package fits maximum-likelihood models using Markov chains on phylogenetic trees.
- Core functions are implemented in C++ for efficiency, with a user-friendly R interface.
Main Results:
- markophylo offers a fast and flexible approach to phylogenetic inference for discrete characters.
- The package enables the application of advanced evolutionary models.
Conclusions:
- markophylo provides a valuable tool for researchers analyzing discrete character evolution on phylogenetic trees.
- The package enhances the efficiency and flexibility of phylogenetic modeling.
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