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Updated: Jul 20, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
PhyloPat: phylogenetic pattern analysis of eukaryotic genes
Tim Hulsen1, Jacob de Vlieg, Peter M A Groenen
1Centre for Molecular and Biomolecular Informatics (CMBI), Nijmegen Centre for Molecular Life Sciences (NCMLS), Radboud University Nijmegen, Nijmegen, The Netherlands. T.Hulsen@cmbi.ru.nl
BMC Bioinformatics
|September 5, 2006
Summary
PhyloPat is a novel webserver enabling phylogenetic pattern queries on the Ensembl gene database. This tool facilitates the identification of genes specific to evolutionary branches or species, enhancing genomic research.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- Phylogenetic patterns analyze gene/protein presence/absence across species.
- These patterns reveal genes unique to specific evolutionary branches.
- Phylogenetic analysis is common for protein databases but not gene databases.
Purpose of the Study:
- Introduce PhyloPat, a webserver for querying the Ensembl gene database using phylogenetic patterns.
- Enable the identification of gene sets specific to evolutionary branches or single species.
Main Methods:
- PhyloPat queries Ensembl orthologies across complete genomes.
- Utilizes a single linkage clustering algorithm for phylogenetic lineages.
- Supports queries via binary patterns or regular expressions, with options for branch-specific patterns and gene ID lookups.
Main Results:
- Analyzed 446,825 genes and 3,164,088 orthologous relationships in EnsMart v40.
- Generated 147,922 reliable phylogenetic lineages.
- Outputs include gene lists (omnipresent, polypresent, oligopresent) and links to functional analysis tools.
Conclusions:
- PhyloPat is the first tool integrating complete genome data with phylogenetic pattern querying.
- Ensembl-derived orthologies ensure reliable phylogenetic lineages.
- The reliability of lineages will improve with future Ensembl releases.
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