Bioinformatics Phylogenetics and Ontology

Analytical and Computational Tools

• HIV Databases
  
  • Branchlength
    Find a root of a phylogenetic tree and estimate the evolutionary rate(s), by either outgrouping, or single or multiple time point optimization.
  • FindModel
    FindModel analyzes your alignment to see which phylogenetic model best describes your data; this model can then be used to generate a better tree.
  • Infer Phylogenetic Relationships and Generate Trees
    The "Quick Tree" option uses PhyML and IRD-defined settings to infer phylogenies based on sequences for datasets of at most 1000 sequences. The "Custom Tree" option offers a choice between the PhyML or RaxML algorithms and the ability to define parameter settings.
  • PhyloPlace/Phylogenetic Placement Service
    To help decide whether a sequence belongs to a known or new clade, this service reports phylogenetic relatedness of a query sequence with reference sequences in known clades. The query sequence is automatically aligned with reference sequences before analysis.
  • PhyML interface
    Provides an interface to PhyML, a fast and flexible program that generates good maximum likelihood trees.
  • Poisson-Fitter
    This tool analyzes sets of homogeneous DNA sequences and performs statistical tests on the Hamming Distance frequency distributions.
  • TreeRate
    Find a root of a phylogenetic tree and estimate the evolutionary rate(s), by either outgrouping, or single or multiple time point optimization.

Databases and Data Sets

• Gene Ontology Finder
  The GO Search tool enables researchers to locate proteins annotated with specified GO criteria.
• ID Mapping Tool
  This tool enables researchers to locate synonymous identifiers across multiple-source databases.
• Immunology Database and Analysis Portal (ImmPORT)
  
  • Cell Type Ontology Browser
  • ImmPORT Gene Lists
• Pathosystems Resource Integration Center (PATRIC)
  
  • Phylogeny Viewer
    Choose an order to view its mulit-gene phylogenetic tree in either phylogram or cladogram format​​​​​​.

Visualization and Modeling Tools

• Infer Phylogenetic Relationships and Generate Trees
  The "Quick Tree" option uses PhyML and IRD-defined settings to infer phylogenies based on sequences for datasets of at most 1000 sequences. The "Custom Tree" option offers a choice between the PhyML or RaxML algorithms and the ability to define parameter settings.
• Neighbor TreeMaker
  This tool takes a nucleotide sequence alignment, converts it to NEXUS format, and uses PAUP to generate a tree, which is displayed using the R Project ape package.