Phylogenetic Analysis

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

Build phylogenetic trees from pairwise distances of sequences and determine the evolutionary relationships between organisms. Estimate synonymous and nonsynonymous substitution rates using maximum likelihood. Visualize and edit phylogenetic tree data in the Phylogenetic Tree app.

Apps

Phylogenetic Tree

Visualize, edit, and explore phylogenetic tree data

Functions

`phytree`	Create phytree object
`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

Objects

phytree object Data structure containing phylogenetic tree

Topics

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.

Featured Examples

Building a Phylogenetic Tree for the Hominidae Species

Construct phylogenetic trees from mtDNA sequences for the Hominidae taxa (also known as pongidae). This family embraces the gorillas, chimpanzees, orangutans and humans.

Open Script

Analyzing the Origin of the Human Immunodeficiency Virus

Construct phylogenetic trees from multiple strains of the HIV and SIV viruses.

Open Script

Bootstrapping Phylogenetic Trees

Generate bootstrap replicates of DNA sequences. The data generated by bootstrapping is used to estimate the confidence of the branches in a phylogenetic tree.

Open Live Script

Using Scoring Matrices to Measure Evolutionary Distance

Handle Scoring Matrices with the sequence alignment tools. The example uses proteins associated with retinoblastoma, a disease caused by a tumor which develops from the immature retina.

Open Live Script