The Building Phylogenetic Tree dialog for the PHYLIP Neighbour-Joining method has the following view:

     <img src="/wiki/download/attachments/4227494/PHYLIP Neighbour-Joining.png"/>

The following parameters are available:

Distance matrix model — model to compute a distance matrix. The following values are available for a nucleotide multiple sequence alignment:

The following models are available for a protein alignment:

Gamma distributed rates across sites — specifies to take into account unequal rates of change at different sites. It is assumed that the distribution of the rates follows the Gamma distribution.

Coefficient of variation of substitution rate among sites — becomes available if the Gamma distributed rates across sites parameter is checked. Specifies the coefficient of the distribution of the rates.

Transition/transversion ratio — expected ratio of transitions to transversions.

To enable bootstrapping check the Bootstrapping and Consensus Trees group check box. The following parameters are available:

Number of replicates — number of replicate date sets.

Seed — random number seed. By default, it is generated automatically. You can manually change this value in order to make results of different runs (of a tree building) reproducible. The should must be an integer greater than zero and less than 32767 and which is of the form 4n+1, that is, it leaves a remainder of 1 when divided by 4. Any odd number can also be used, but may result in a random number sequence that repeats itself after less than the full one billion numbers. Usually this is not a problem.

Consensus type — specifies the method to build the consensus tree. Select one of the following:

Fraction — becomes available when the Consensus type parameter is set to M1. Specifies the fraction.

Display tree in new window - displays tree in new window.

Display tree with alignment editor - displays tree with alignment editor.

Synchronize alignment with tree - synchronize alignment and tree.

Save tree to — file to save the tree built.

Press the Build button to build a tree with the parameters selected.