PhyloPat

PhyloPat analyzes phylogenetic presence–absence patterns across the complete Ensembl gene database using orthologies from EnsMart v40 to identify lineage-specific genes and construct phylogenetic lineages.

Key Features:

• Phylogenetic Pattern Analysis: Identification of gene presence or absence across species based on analysis of 446,825 genes and 3,164,088 orthologous relationships within EnsMart v40.
• Single Linkage Clustering Algorithm: Construction of 147,922 phylogenetic lineages from Ensembl orthologies using a single linkage clustering algorithm.
• Flexible Query Options: Support for binary phylogenetic patterns, regular expressions, and selection of specific branches within a phylogenetic tree of 21 included species to generate branch-specific patterns.
• Gene Lineage Identification: Determination of phylogenetic lineage for input lists of Ensembl or EMBL identifiers.
• Output Formats and Functional Integration: Export of results in HTML, Excel, or plain text formats with integrated links to the FatiGO web interface for functional information.
• Gene Presence Categories: Classification and reporting of omnipresent, polypresent, and oligopresent gene lists across the surveyed species.

Scientific Applications:

• Comparative Genomics: Detection of lineage-specific and conserved genes across multiple species for comparative genomic analyses.
• Functional Genomics: Integration of phylogenetic patterns with FatiGO-linked functional data to explore gene function in an evolutionary context.
• Evolutionary Biology: Reconstruction and analysis of phylogenetic lineages to study gene evolution and orthology relationships.

Methodology:

Utilizes orthologies generated by the Ensembl orthology pipeline from EnsMart v40 and applies a single linkage clustering algorithm to construct 147,922 phylogenetic lineages from 3,164,088 orthologous relationships among 446,825 genes across 21 species.