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Manipulating biological data
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Manipulating biological data
Sequences and Alignments
Genetic code
Trees
Tables
Building alignments
Using the cogent3 aligners
Converting gaps from aa-seq alignment to nuc seq alignment
Genetic distance calculation
Fast pairwise distance estimation
Computing genetic distances using the
Alignment
object
Using the distance calculator directly
Likelihood based pairwise distance estimation
Building phylogenies
Building A Phylogenetic Tree From Pairwise Distances
Directly via
alignment.quick_tree()
By Least-squares
By ML
Evolutionary Analysis Using Likelihood
Specifying substitution models
Making a likelihood function
Useful Utilities
UnionDict
– a dict with set like operations and keys as attributes
Using Cogent3’s optimisers for your own functions
Miscellaneous functions