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Phylogenetic Analysis

Reconstruct, view, interact with, and edit phylogenetic trees; bootstrap methods for confidence assessment; synonymous and nonsynonymous analysis

Functions

seqlinkage Construct phylogenetic tree from pairwise distances
seqneighjoin Construct phylogenetic tree using neighbor-joining method
seqpdist Calculate pairwise distance between sequences
phytreeviewer Visualize, edit, and explore phylogenetic tree data
dnds Estimate synonymous and nonsynonymous substitution rates
dndsml Estimate synonymous and nonsynonymous substitution rates using maximum likelihood method
gethmmtree Retrieve phylogenetic tree data from PFAM database
seqinsertgaps Insert gaps into nucleotide or amino acid sequence

Classes

phytree Create phytree object
phytree object Data structure containing phylogenetic tree

Examples and How To

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