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Create phytree object

* Tree* = phytree(

`B`

`Tree`

`B`

`D`

`Tree`

`B`

`C`

`Tree`

= phytree(`BC`

)

`Tree`

= phytree(..., `N`

)

`Tree`

`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. |

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`

`[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`

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`

`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

`cluster`

| `get`

| `getbyname`

| `getcanonical`

| `getmatrix`

| `getnewickstr`

| `pdist`

| `phytreeread`

| `phytreeviewer`

| `phytreewrite`

| `plot`

| `prune`

| `reroot`

| `select`

| `seqlinkage`

| `seqneighjoin`

| `seqpdist`

| `subtree`

| `view`

| `weights`

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