phytree
Create phytree object
Syntax
Tree
= phytree(B
)
Tree
= phytree(B
, D
)
Tree
= phytree(B
, C
)
Tree
= phytree(BC
)
Tree
= phytree(..., N
)
Tree
= phytree
Arguments
B | Numeric array of size |
C | Column vector with distances for every branch. |
D | Column vector with distances from every node to their parent branch. |
BC | Combined matrix with pointers to branches or leaves, and distances of branches. |
| Cell array with the names of leaves and branches. |
Description
creates
an ultrametric phylogenetic tree object. In an ultrametric phylogenetic
tree object, all leaves are the same distance from the root.Tree
= phytree(B
)
B
is a numeric array of size [NUMBRANCHES
X 2]
in which every row represents a branch of the tree
and it contains two pointers to the branch or leaf nodes, which are
its children.
Leaf nodes are numbered from 1
to NUMLEAVES
and
branch nodes are numbered from NUMLEAVES + 1
to
NUMLEAVES + NUMBRANCHES
. Note that because only
binary trees are allowed, NUMLEAVES = NUMBRANCHES + 1
.
Branches are defined in chronological order (for example, B(i,:)
> NUMLEAVES + i
). As a consequence, the first row can
only have pointers to leaves, and the last row must represent the
root branch. Parent-child distances are set to 1
,
unless the child is a leaf and to satisfy the ultrametric condition
of the tree its distance is increased.
Given a tree with three leaves and two branches as an example.
In the MATLAB® Command Window, type
B = [1 2 ; 3 4] B = 1 2 3 4 tree = phytree(B) Phylogenetic tree object with 3 leaves (2 branches) view(tree)
creates
an additive (ultrametric or nonultrametric) phylogenetic tree object
with branch distances defined by Tree
= phytree(B
, D
)D
. D
is
a numeric array of size [NUMNODES X 1]
with the
distances of every child node (leaf or branch) to its parent branch
equal to NUMNODES = NUMLEAVES + NUMBRANCHES
. The
last distance in D
is the distance of the
root node and is meaningless.
b = [1 2 ; 3 4 ] b = 1 2 3 4 d = [1; 2; 1.5; 1; 0] d = 1.0000 2.0000 1.5000 1.0000 0 view(phytree(b,d))
creates
an ultrametric phylogenetic tree object with distances between branches
and leaves defined by Tree
= phytree(B
, C
)C
. C
is
a numeric array of size [NUMBRANCHES X 1]
, which
contains the distance from each branch to the leaves. In ultrametric
trees, all of the leaves are at the same location (same distance to
the root).
b = [1 2 ; 3 4] b = 1 2 3 4 c = [1 4]' c = 1 4 view(phytree(b,c))
creates
an ultrametric phylogenetic binary tree object with branch pointers
in Tree
= phytree(BC
)BC(:,[1 2])
and branch coordinates in BC(:,3)
.
Same as phytree(B,C)
.
specifies the names for the leaves and/or the branches. Tree
= phytree(..., N
)N
is
a string vector or cell array of character vectors. If
NUMEL(N)==NUMLEAVES
, then the names are assigned chronologically
to the leaves. If NUMEL(N)==NUMBRANCHES
, the names are assigned to
the branch nodes. If NUMEL(N)==NUMLEAVES + NUMBRANCHES
, all the nodes
are named. Unassigned names default to 'Leaf #'
and/or
'Branch #'
as required.
creates
an empty phylogenetic tree object.Tree
= phytree
Examples
Version History
Introduced in R2006a
See Also
phytreeread
| phytreeviewer
| phytreewrite
| seqlinkage
| seqneighjoin
| seqpdist
| cluster
| get
| getbyname
| getcanonical
| getmatrix
| getnewickstr
| pdist
| plot
| prune
| reroot
| select
| subtree
| view
| weights