Phylogenetic Analysis

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

Apps

Phylogenetic Tree

Visualize, edit, and explore phylogenetic tree data

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

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

Reconstructing the Origin and the Diffusion of the SARS Epidemic

An analysis of the origin and diffusion of the SARS epidemic. It is based on the discussion of viral phylogeny presented in Chapter 7 of "Introduction to Computational Genomics. A Case Studies Approach" [1].

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

Analyzing the Human Distal Gut Microbiome

Several ways of visualizing the results of functional metagenomic analyses. The discussion is based on two studies focusing on the metagenomic analysis of the human distal gut microbiome.

Open 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