PhylomeDB

PhylomeDB provides a repository of genome-wide gene phylogenies (phylomes) and associated annotations to enable evolutionary analysis of genes across species.

Key Features:

• Extensive Data Repository: Hosts over 8 million phylogenetic trees and orthology/paralogy relationships covering genes from more than 6,000 species, including Homo sapiens, Saccharomyces cerevisiae, Escherichia coli, Arabidopsis thaliana, Candida albicans, and Acyrthosiphon pisum.
• High-Quality Phylogenetic Analysis: Uses a phylogenetic pipeline that includes evolutionary model testing, alignment trimming, and Maximum Likelihood tree inference to produce genome-wide phylogenies.
• Annotated Sequences and Alignments: Provides annotated sequences and multiple-sequence alignments associated with each gene phylogeny.
• Functional and Structural Annotations: Phylogenetic trees are annotated with taxonomic information, protein-domain arrangements, functional annotations, and evolutionary insights.

Scientific Applications:

• Orthology and Paralogy Inference: Supports inference and prediction of orthology and paralogy relationships across genomes.
• Gene Duplication Dating: Enables dating of gene duplication events using reconstructed gene trees.
• Gene Family Evolution: Facilitates detection of gene family expansions and contractions.
• Horizontal Transfer and Recombination Detection: Aids in identifying horizontal gene transfer and recombination events from phylogenetic patterns.
• Incomplete Lineage Sorting and Reticulate Evolution: Supports analyses revealing incomplete lineage sorting, introgression, and gene conversion.
• Genome and Transcriptome Analysis: Provides reference phylogenomic data for analysis of newly sequenced genomes and transcriptomes.
• Selection and Evolutionary Insight: Enables investigation of selection and other evolutionary processes using annotated phylogenies.

Methodology:

Phylogenies are produced by evolutionary model testing, alignment trimming, and Maximum Likelihood tree inference; trees and associated sequences/alignments are annotated with taxonomic information, protein-domain arrangements, functional annotations, and orthology/paralogy relationships.