| Calling Sequence
| GapTree(msa,...)
|
| Parameters
| | Name | Type | Description |
|
| msa
| MAlignment | one or many MAlignments over the same species |
|
| Return Type
| Tree |
| Globals
| GapTree_Title, |
| Synopsis
| GapTree builds a phylogenetic tree based on the
gaps of one/several multiple sequence alignments.
The assumption is that gap creation is a sufficiently
rare which allows us to build better trees for longer
distances.
The gaps are extracted from MAlignments given as arguments.
Only single gaps which are clearly delimited are used.
Areas in which no sequence is gap-less are not considered.
Areas where sequences have two gaps are also discarded.
The existence/non-existence of gaps is then fed to a
parsimony algorithm to produce a tree.
The input MAlignments should be on the same set of
labels. More specifically, we expect the MAlignments to
be over different sets of sequences belonging to the same
set of species, identified by the same list of labels. |
| The global variable GapTree_Title is set to
a short description of the details of the construction.
|
| See also
| BootstrapTree, DrawTree, Entry, Leaf, LeastSquaresTree, MAlignment, Sequence, SignedSynteny, Synteny, Tree |