NGphylogeny.fr

NGphylogeny.fr reconstructs and analyzes phylogenetic relationships among molecular sequences for evolutionary inference.

Key Features:

• Integrated tool suite: Integration of bioinformatics software including TNT, FastME, MrBayes, PhyML, SMS, FastTree, trimAl, and BOOSTER, with tools maintained in their latest versions.
• Sequence searching: Support for sequence searching as part of phylogenetic workflows.
• Multiple sequence alignment: Support for multiple sequence alignment and alignment processing.
• Model selection: Support for model selection, including use of SMS (Smart Model Selection).
• Tree inference: Support for tree inference using distance-based methods, parsimony, maximum likelihood, and Bayesian inference.
• Tree visualization: Support for tree visualization and downstream tree analyses.
• Phylogenetic methods: Explicit support for distance-based approaches, parsimony, maximum likelihood, and Bayesian inference.
• Workflow management: Use of the Galaxy workflow system to manage and execute workflows.
• Scalability: Capacity to handle a large volume of jobs and process substantial datasets.

Scientific Applications:

• Phylogenetic reconstruction: Reconstruction of evolutionary relationships among molecular sequences using distance, parsimony, maximum likelihood, or Bayesian methods.
• Model testing and selection: Selection and testing of evolutionary models for sequence-based analyses.
• Alignment-based comparative analyses: Comparative sequence analyses based on multiple sequence alignment and alignment trimming.
• Large-scale phylogenomic analyses: Analysis of substantial datasets and high-throughput phylogenetic jobs.
• Tree visualization and interpretation: Visualization and interpretation of inferred phylogenetic trees.

Methodology:

Galaxy workflow system for workflow management and execution; integration of TNT, FastME, MrBayes, PhyML, SMS, FastTree, trimAl, and BOOSTER; support for sequence searching, multiple sequence alignment, model selection, tree inference, tree visualization, and distance-based, parsimony, maximum likelihood, and Bayesian inference.