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
  • 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.

Contact Information

For more information on Bioinformatics Phylogenetics and Ontology, email:
Bioinformatics and Computational Sciences Branch

Content last reviewed on January 24, 2013