| Bioinformatics Toolbox™ | |
Method Reference |  Alphabetical List |
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Following are methods for use with a phytree object.
| 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 |
Following are methods for use with a biograph object.
| allshortestpaths (biograph) | Find all shortest paths in biograph object |
| conncomp (biograph) | Find strongly or weakly connected components in biograph object |
| dolayout (biograph) | Calculate node positions and edge trajectories |
| getancestors (biograph) | Find ancestors in biograph object |
| getdescendants (biograph) | Find descendants in biograph object |
| getedgesbynodeid (biograph) | Get handles to edges in biograph object |
| getmatrix (biograph) | Get connection matrix from biograph object |
| getnodesbyid (biograph) | Get handles to nodes |
| getrelatives (biograph) | Find relatives in biograph object |
| isdag (biograph) | Test for cycles in biograph object |
| isomorphism (biograph) | Find isomorphism between two biograph objects |
| isspantree (biograph) | Determine if tree created from biograph object is spanning tree |
| maxflow (biograph) | Calculate maximum flow in biograph object |
| minspantree (biograph) | Find minimal spanning tree in biograph object |
| shortestpath (biograph) | Solve shortest path problem in biograph object |
| topoorder (biograph) | Perform topological sort of directed acyclic graph extracted from biograph object |
| traverse (biograph) | Traverse biograph object by following adjacent nodes |
| view (biograph) | Draw figure from biograph object |
Following are methods for use with a geneont object.
| getancestors (geneont) | Find terms that are ancestors of specified Gene Ontology (GO) term |
| getdescendants (geneont) | Find terms that are descendants of specified Gene Ontology (GO) term |
| getmatrix (geneont) | Convert geneont object into relationship matrix |
| getrelatives (geneont) | Find terms that are relatives of specified Gene Ontology (GO) term |
Following are methods for use with a clustergram object.
| get (clustergram) | Retrieve information about clustergram object |
| plot (clustergram) | Render clustergram heat map and dendrograms for clustergram object |
| set (clustergram) | Set property of clustergram object |
| view (clustergram) | View clustergram heat map and dendrograms for clustergram object |
| zonebackadj | Methods — Alphabetical List | |
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