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Updated: Oct 25, 2025
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
16.1K
PhyloFisher: A phylogenomic package for resolving eukaryotic relationships.
Alexander K Tice1,2, David Žihala3, Tomáš Pánek1,3
1Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America.
Plos Biology
|August 6, 2021
Summary
PhyloFisher software aids phylogenomic analysis by providing a curated eukaryotic gene database and tools to build robust evolutionary trees. It helps detect paralogs, improving the accuracy of phylogenetic datasets.
Area of Science:
- Evolutionary Biology
- Bioinformatics
- Genomics
Background:
- Phylogenomic analyses using hundreds of protein-coding genes are common for resolving evolutionary relationships.
- Existing software lacks integrated tools for dataset construction, analysis, and validation.
- High-quality curated databases for deep eukaryotic evolutionary relationships (>100 million years) are unavailable.
Purpose of the Study:
- To develop user-friendly software (PhyloFisher) for phylogenomic dataset construction and analysis.
- To create a manually curated database of eukaryotic protein-coding genes for phylogenetic studies.
- To provide tools for robust phylogenetic analyses and assessment of evolutionary relationships.
Main Methods:
- Developed PhyloFisher software in Python 3.
- Created a curated database of 240 protein-coding genes from 304 eukaryotic taxa.
- Implemented novel ortholog selection tools and utilities for phylogenomic analyses.
- Performed phylogenetic reconstructions for the tree of eukaryotes and Saccharomycetaceae.
Main Results:
- Demonstrated the utility of PhyloFisher for phylogenetic reconstructions across diverse eukaryotic groups and evolutionary timescales.
- Showcased that common methods can inadvertently include paralogs in phylogenomic datasets.
- Highlighted PhyloFisher's ability to detect paralog inclusions, enhancing orthology assignment accuracy.
Conclusions:
- PhyloFisher provides a comprehensive workflow for robust phylogenomic analyses.
- The curated database and tools improve the accuracy of evolutionary relationship assessments.
- The software facilitates informed orthology decisions, leading to more reliable phylogenetic datasets.
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