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.
- Branchlength
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.
- Phylogeny Viewer
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