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Sequence types accepted by various Datamonkey components. Available analyses are automatically determined by the server based on the contents of the alignment and user description from the upload page.
Analysis Sequence type Comments
Neighbor Joining tree reconstruction Nucleotide/Protein/Codon TN93 distance is used for N and C data. Corrected p-distance is used for P data
Model selection Nucleotide/Protein/Codon All 4x4 reversible 203 models are tried for N and C data. An a priori list of empirical models is tried for P data.
SLAC Codon
FEL/IFEL Codon
REL Codon
PARRIS Codon
GABranch Codon Recombinant data are not allowed.
Spidermonkey/BGM Nucleotide/Protein/Codon Recombinant data are not allowed. All substitutions are used for N and P data. Only non-synonymous substitutions are used for C data.
GARD and SBP Nucleotide/Protein
Ancestral State Reconstruction Nucleotide/Protein/Codon Requires a rooted tree. Recombinant data are handled.
DEPS Protein Requires a rooted tree.
Codon Model Selection Codon
Evolutionary Fingerprinting Codon
UCSD Viral Evolution Group 2004-2017  
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