## Documentation Center |

Construct phylogenetic tree using neighbor-joining method

* PhyloTree* = seqneighjoin(

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

Method | String 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 strings
. Distances |

`PhyloTree = seqneighjoin(Distances)` computes

`PhyloTree = seqneighjoin(Distances, Method)` specifies

D(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). |

`PhyloTree = seqneighjoin(Distances, Method, Names)` passes

`PhyloTree = seqneighjoin(...,
'Reroot', RerootValue)` specifies
whether to reroot

[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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