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.