4.5 BppDist: Bio++ Distance Methods

The BppDist program uses the common syntax introduced in the previous section for setting the alphabet, loading the sequences (see Sequences) and tree (see Tree) and specifying the model (see Model, only the section corresponding to the homogeneous case).

Specific options are:

output.matrix.file = {{path}|none}

Where to write the matrix file (only philip format supported for now).

method = {wpgma|upgma|nj|bionj}

The algorithm to use to build the tree.

optimization.method = {init|pairwise|iterations}

There are several ways to optimize substitution parameters. The init option corresponds to the standard behavior, that is, keeping them to their initial, user-provided value. The pairwise option estimate those parameters in a pairwise manner. This should be avoided, particularly with parameter-rich models. Finally the iterations option corresponds to Ninio et al, Bioinformatics (2007) recursive algorithm: After each distance tree, a global ML estimation of the substitution parameters is performed. The estimated values are then used to rebuild a distance matrix and a tree. The algorithm stops when the topology does not change anymore. The ML optimization uses the parameters described in (see Estimation).

output.tree.file = {{path}|none}

The final tree, possibly with bootstrap values: BppDist uses the same options for bootstrap analysis than the BppML program (see bppml).