PhyloFisher

PhyloFisher constructs and analyzes phylogenomic datasets of protein sequences to resolve deep eukaryotic evolutionary relationships.

Key Features:

• Curated Database: A manually curated set of 240 protein-coding genes from 304 eukaryotic taxa covering broad eukaryotic diversity and deep evolutionary relationships (>100 million years).
• Ortholog Selection Tool: A dedicated ortholog selection component to identify true orthologs and minimize paralog contamination in datasets.
• Diverse Analytical Utilities: A suite of utilities for dataset construction and phylogenetic analysis of protein-sequence phylogenomic datasets.
• Validation Strategies: Multiple validation strategies to assess the robustness of phylogenetic datasets and reconstructions.
• Implementation: Implemented in Python 3.

Scientific Applications:

• Eukaryotic tree reconstruction: Reconstruction of the tree of eukaryotes using protein-coding gene datasets.
• Saccharomycetaceae analysis: Phylogenomic analysis of the Saccharomycetaceae clade of budding yeasts.
• Broad phylogenetic studies: Addressing phylogenetic questions across a wide range of evolutionary timescales and organismal diversity.

Methodology:

PhyloFisher aids detection of paralog inclusions that can arise from all vs. all BLAST searches followed by Markov Cluster Algorithm (MCL) clustering and from automated tree pruning algorithms, thereby informing orthology assignments.