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