Phylogeny.fr

Phylogeny.fr reconstructs phylogenetic trees and facilitates analysis of evolutionary relationships among molecular sequences.

Key Features:

• Automated Phylogeny Pipeline: Chains sequence alignment, phylogenetic tree construction, and graphical rendering and provides three operational modes: 'One Click' (MUSCLE, PhyML, TreeDyn), 'Advanced' (parameter customization), and 'A la Carte' (custom pipeline composition).
• Sequence Collection and Analysis: Performs BLAST searches against general or specialized databases and uses a guide tree to select neighbor homologous sequences for input into the phylogeny pipeline.
• BLAST-Explorer Integration: Integrates BLAST-Explorer to enhance BLAST searches, enable phylogeny-oriented sequence retrieval with flexible selection criteria, and provide enriched BLAST outputs for dataset construction.

Scientific Applications:

• Phylogenetic reconstruction: Reconstruction of evolutionary relationships among genes, proteins, or other molecular sequences.
• Molecular evolution analyses: Tree-based analyses to study evolutionary patterns and relationships.
• Dataset construction for phylogenetics: Assembly of homologous sequence datasets using BLAST and BLAST-Explorer for downstream phylogenetic inference.

Methodology:

Chains MUSCLE for multiple sequence alignment, PhyML for phylogenetic tree construction, TreeDyn for tree rendering, and integrates BLAST and BLAST-Explorer for homologous sequence retrieval and guide-tree-based neighbor selection.