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Phylogenetic Analysis

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


Phylogenetic Tree Visualize, edit, and explore phylogenetic tree data


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


phytree Create phytree object
phytree object Data structure containing phylogenetic tree

Examples and How To

Building a Phylogenetic Tree

Using data from mitochondrial D-loop sequences, create a phylogenetic tree for a family of primates.


Phylogenetic Analysis

Phylogenetic analysis is the process you use to determine the evolutionary relationships between organisms.

Using the Phylogenetic Tree App

Description of menu commands and features for creating publishable tree figures.

Sequence Utilities and Statistics

You can manipulate and analyze your sequences to gain a deeper understanding of the physical, chemical, and biological characteristics of your data.

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