4.8 BppPhySamp: Bio++ Phylogenetic Sampler

The Bio++ Phylogenetic Sampler samples sequences from a file according to phylogenetic information. The goal is to clean a big data set by removing redundant sequences, bringing only few additional information for evolutionary analyses.

The BppPhySamp programs uses the common options for setting the alphabet, loading the sequences (see Sequences) and (see Tree) and writing the resulting data set (see WritingSequences, see WritingTrees).

input.method = {tree|matrix}

The method to provide phylogenetic information, either by a tree or a matrix. If the tree option is used, then the options for reading trees are used (see Tree).

input.matrix = {path} [[input.method = matrix]]

The input matrix file.

deletion_method = {random|threshold|sample}

Method to use to remove sequence.

threshold = {float>0} [[deletion_method = threshold ]]

The minimum distance separating two sequences in the sampled data set. Any sequences closer than this threshold in the original data set will be confronted so that only one is kept.

sample_size = {int>0} [[deletion_method = sample|random ]]

The number of sequences to keep in the final data set.

choice_criterion = {length|length.complete|random}

How to chose between closely related sequences? length takes the longest (maximum number of non-gap positions), length.complete takes the sequence with the maximum number of fully resolved positions and random picks one sequence at random.