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Construct phylogenetic tree using neighbor-joining method

* PhyloTree* = seqneighjoin(

`Distances`

`PhyloTree`

`Distances`

`Method`

`PhyloTree`

`Distances`

`Method`

`Names`

`PhyloTree`

`RerootValue`

`Distances` | Matrix or vector containing biological distances between pairs
of sequences, such as returned by the `seqpdist` function. |

`Method` | Character vector specifying a method to compute the distances
between nodes. Choices are `'equivar'` (default)
or `'firstorder'` . |

`Names` | Either of the following: Vector of structures with the fields `Header` and`Name` Cell array of character vectors
. `Distances` |

computes * PhyloTree* = seqneighjoin(

`Distances`

`PhyloTree`

`Distances`

specifies * PhyloTree* = seqneighjoin(

`Distances`

`Method`

`Method`

`n`

, after joining `i`

and `j`

and
all other nodes (`k`

), is given byD(n,k) = a*D(i,k) + (1-a)*D(j,k) - a*D(n,i) - (1-a)*D(n,j)

This expression is guaranteed to find the correct tree with additive data (minimum variance reduction).

Choices for * Method* are:

Method | Description |
---|---|

`equivar` (default) | Assumes equal variance and independence of evolutionary distance estimates (a = 1/2), such as in the original neighbor-joining algorithm by Saitou and Nei, JMBE (1987) or as in Studier and Keppler, JMBE (1988). |

`firstorder` | Assumes a first-order model of the variances and covariances
of evolutionary distance estimates, with `'a'` being
adjusted at every iteration to a value between `0` and `1` ,
such as in Gascuel, JMBE (1997). |

passes * PhyloTree* = seqneighjoin(

`Distances`

`Method`

`Names`

`Names`

specifies
whether to reroot * PhyloTree* = seqneighjoin(...,
'Reroot',

`RerootValue`

`PhyloTree`

`true`

(default)
or `false`

. When `RerootValue`

`false`

, `seqneighjoin`

excludes
rerooting the resulting tree, which is useful for observing the original
linkage order followed by the algorithm. By default `seqneighjoin`

reroots
the resulting tree using the midpoint method. [1] Saitou, N., and Nei, M. (1987). The neighbor-joining
method: A new method for reconstructing phylogenetic trees. Molecular
Biology and Evolution *4(4)*, 406–425.

[2] Gascuel, O. (1997). BIONJ: An improved
version of the NJ algorithm based on a simple model of sequence data.
Molecular Biology and Evolution *14* 685–695.

[3] Studier, J.A., Keppler, K.J. (1988). A
note on the neighbor-joining algorithm of Saitou and Nei. Molecular
Biology and Evolution *5(6)* 729–731.

`cluster`

| `multialign`

| `phytree`

| `plot`

| `reroot`

| `seqlinkage`

| `seqpdist`

| `view`

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