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| R2012a Documentation → Bioinformatics Toolbox | |
Learn more about Bioinformatics Toolbox |
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| Contents | Index |
A phytree object is a data structure containing a phylogenetic tree. Phylogenetic trees are binary rooted trees, which means that each branch is the parent of two other branches, two leaves, or one branch and one leaf. A phytree object can be ultrametric or nonultrametric.
Following are methods of a phytree object:
| cluster (phytree) | Validate clusters in phylogenetic tree |
| get (phytree) | Retrieve information about phylogenetic tree object |
| getbyname (phytree) | Branches and leaves from phytree object |
| getcanonical (phytree) | Calculate canonical form of phylogenetic tree |
| getmatrix (phytree) | Convert phytree object into relationship matrix |
| getnewickstr (phytree) | Create Newick-formatted string |
| pdist (phytree) | Calculate pairwise patristic distances in phytree object |
| plot (phytree) | Draw phylogenetic tree |
| prune (phytree) | Remove branch nodes from phylogenetic tree |
| reorder (phytree) | Reorder leaves of phylogenetic tree |
| reroot (phytree) | Change root of phylogenetic tree |
| select (phytree) | Select tree branches and leaves in phytree object |
| subtree (phytree) | Extract phylogenetic subtree |
| view (phytree) | View phylogenetic tree |
| weights (phytree) | Calculate weights for phylogenetic tree |
Note You cannot modify these properties directly. You can access these properties using the get method. |
| Property | Description |
|---|---|
| NumLeaves | Number of leaves |
| NumBranches | Number of branches |
| NumNodes | Number of nodes (NumLeaves + NumBranches) |
| Pointers | Branch to leaf/branch connectivity list |
| Distances | Edge length for every leaf/branch |
| LeafNames | Names of the leaves |
| BranchNames | Names of the branches |
| NodeNames | Names of all the nodes |
cluster | get | getbyname | getcanonical | getmatrix | getnewickstr | pdist | phytree | phytreeread | phytreetool | phytreewrite | plot | prune | reroot | select | seqlinkage | seqneighjoin | seqpdist | subtree | view | weights
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