Phylogenetic Analysis
Phylogenetic analysis is the process you use to determine the evolutionary relationships between organisms. The results of an analysis can be drawn in a hierarchical diagram called a cladogram or phylogram (phylogenetic tree). The branches in a tree are based on the hypothesized evolutionary relationships (phylogeny) between organisms. Each member in a branch, also known as a monophyletic group, is assumed to be descended from a common ancestor. Originally, phylogenetic trees were created using morphology, but now, determining evolutionary relationships includes matching patterns in nucleic acid and protein sequences. The Bioinformatics Toolbox™ provides the following data structure and functions for phylogenetic analysis.
Phylogenetic tree data —
Read and write Newick-formatted tree files (phytreeread
, phytreewrite
) into the MATLAB® Workspace
as phylogenetic tree objects (phytree
).
Create a phylogenetic tree —
Calculate the pairwise distance between biological sequences (seqpdist
), estimate the substitution
rates (dnds
, dndsml
), build a phylogenetic tree from
pairwise distances (seqlinkage
, seqneighjoin
, reroot
),
and view the tree in an interactive GUI that allows you to view, edit,
and explore the data (phytreeviewer
or view
).
This GUI also allows you to prune branches, reorder, rename, and explore
distances.
Phylogenetic tree object methods —
You can access the functionality of the phytreeviewer
user
interface using methods for a phylogenetic tree object (phytree
). Get property values (get
)
and node names (getbyname
). Calculate
the patristic distances between pairs of leaf nodes (pdist
, weights
)
and draw a phylogenetic tree object in a MATLAB Figure window
as a phylogram, cladogram, or radial treeplot (plot
).
Manipulate tree data by selecting branches and leaves using a specified
criterion (select
, subtree
)
and removing nodes (prune
). Compare trees (getcanonical
)
and use Newick-formatted strings (getnewickstr
).