Ensembl Compara

Ensembl Compara provides cross-species comparative genomics at sequence and gene levels, enabling gene tree reconstruction and ortholog prediction.

Key Features:

• GeneTrees: A comprehensive phylogenetic resource focused on gene-oriented analyses.
• Phylogenetic pipeline: Performs clustering, multiple alignment, and generation of phylogenetic trees for large gene families.
• Non-sequence-based correctness metrics: Implements two novel non-sequence-based metrics to assess the correctness of gene trees.
• TreeBeST benchmarking: Benchmarking shows the TreeBeST method from TreeFam exhibits superior performance in generating accurate gene trees.
• Phylogeny-based orthology inference: Uses phylogenetic approaches that enhance ortholog prediction and increase coverage compared with traditional clustering methods.

Scientific Applications:

• Cross-species comparative genomics: Comparative analyses at sequence and gene levels across multiple species.
• Gene-oriented phylogenetics: Reconstruction and analysis of gene family phylogenies using GeneTrees.
• Ortholog prediction: Identification of orthologs across diverse species using phylogeny-informed methods.
• Phylogenetic accuracy assessment: Evaluation of gene tree correctness using the two non-sequence-based metrics and benchmarking results.

Methodology:

Computational steps explicitly include clustering of gene families, multiple sequence alignment, generation of phylogenetic trees, calculation of two non-sequence-based gene-tree correctness metrics, and application/benchmarking of the TreeBeST method from TreeFam.