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Phylogenetic Analysis

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

Apps

Phylogenetic TreeVisualize, edit, and explore phylogenetic tree data

Functions

seqlinkageConstruct phylogenetic tree from pairwise distances
seqneighjoinConstruct phylogenetic tree using neighbor-joining method
seqpdistCalculate pairwise distance between sequences
phytreeviewerVisualize, edit, and explore phylogenetic tree data
dndsEstimate synonymous and nonsynonymous substitution rates
dndsmlEstimate synonymous and nonsynonymous substitution rates using maximum likelihood method
gethmmtreeRetrieve phylogenetic tree data from PFAM database
seqinsertgapsInsert gaps into nucleotide or amino acid sequence

Classes

phytreeCreate phytree object
phytree objectData structure containing phylogenetic tree

Examples and How To

Building a Phylogenetic Tree for the Hominidae Species

This example shows how to construct phylogenetic trees from mtDNA sequences for the Hominidae taxa (also known as pongidae).

Concepts

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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