Package edu.rit.compbio.phyl

Package edu.rit.compbio.phyl contains parallel programs for phylogenetic tree construction. For further information, see:

- J. Felsenstein. Inferring Phylogenies. Sinauer Associates, 2004.

The following program constructs a phylogenetic tree of DNA sequences using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm:

- Class Upgma

The following program constructs maximum parsimony phylogenetic trees of DNA sequences using exhaustive search:

- Class PhylogenyParsExhSeq

The following programs construct maximum parsimony phylogenetic trees of DNA sequences using branch-and-bound search:

- Class PhylogenyParsBnbSeq
- Class PhylogenyParsBnbSmp

The following program draws a picture of a phylogenetic tree:

- Class DrawTree

The other classes are used by the above programs.