PhyloCloud

PhyloCloud facilitates interactive analysis, annotation, and visualization of large collections of phylogenetic trees and multiple sequence alignments for phylogenomic research.

Key Features:

• Tree and MSA integration: Visualizes and links phylogenetic trees with multiple sequence alignments for combined inspection and annotation.
• Node annotation: Supports annotation of internal and terminal nodes within phylogenetic trees.
• Searching: Provides search capabilities across tree collections and associated metadata.
• Topology editing: Enables editing of tree topologies.
• Automatic tree rooting: Implements automatic rooting of phylogenetic trees.
• Orthology detection: Performs orthology detection on gene trees.
• Phylogeny construction workflows: Constructs new phylogenies using fast, predefined workflows.
• Graphical topology comparison: Compares different tree topologies using graphical methods.
• Taxonomic database queries: Queries taxonomic resources such as NCBI (National Center for Biotechnology Information) and GTDB (Genome Taxonomy Database).
• Visualization engine: Uses the ETE Toolkit v4.0 for scalable visualization of very large phylogenetic trees with custom annotations and aligned sequences.
• Data sharing and repository: Stores and shares tree collections and specific views, supporting public and private access modes.

Scientific Applications:

• Phylogenomic dataset exploration: Exploration and inspection of hundreds to thousands of phylogenetic trees from genome-wide projects.
• Evolutionary and orthology analyses: Detection of orthologous relationships and analysis of gene family evolution.
• Comparative topology analysis: Graphical comparison and evaluation of alternative tree topologies.
• Taxonomic integration: Assignment and validation of taxonomy using NCBI and GTDB references.
• Annotation-driven interpretation: Integration of node annotations and MSAs to interpret complex phylogenetic patterns.
• Data distribution and reuse: Provision of a repository for sharing phylogenomic datasets and curated tree collections.

Methodology:

Visualization with ETE Toolkit v4.0; node annotation; search and topology editing; automatic tree rooting; orthology detection; construction of phylogenies via fast predefined workflows; graphical topology comparison; querying NCBI and GTDB; integration of multiple sequence alignments.