Documentation 
Construct phylogenetic tree using neighborjoining method
PhyloTree = seqneighjoin(Distances)
PhyloTree = seqneighjoin(Distances, Method)
PhyloTree = seqneighjoin(Distances, Method, Names)
PhyloTree = seqneighjoin(...,
'Reroot', RerootValue)
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:

PhyloTree = seqneighjoin(Distances) computes PhyloTree, a phylogenetic tree object, from Distances, pairwise distances between the species or products, using the neighborjoining method.
PhyloTree = seqneighjoin(Distances, Method) specifies Method, a method to compute the distances of the new nodes to all other nodes at every iteration. The general expression to calculate the distances between the new node, n, after joining i and j and all other nodes (k), is given by
D(n,k) = a*D(i,k) + (1a)*D(j,k)  a*D(n,i)  (1a)*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 neighborjoining algorithm by Saitou and Nei, JMBE (1987) or as in Studier and Keppler, JMBE (1988). 
firstorder  Assumes a firstorder 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 Names, a list of names (such as species or products), to label the leaf nodes in the phylogenetic tree object.
PhyloTree = seqneighjoin(...,
'Reroot', RerootValue) specifies
whether to reroot PhyloTree. Choices are true (default)
or false. When RerootValue is 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 neighborjoining 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 neighborjoining algorithm of Saitou and Nei. Molecular Biology and Evolution 5(6) 729–731.
cluster  multialign  phytree  plot  reroot  seqlinkage  seqpdist  view