Package edu.rit.compbio.phyl

Package edu.rit.compbio.phyl contains parallel programs for phylogenetic tree construction.

See: Description

Interface Summary

Interface	Description
Distance	Interface Distance specifies the interface for an object that computes the distance between two DnaSequences.

Class Summary

Class	Description
DnaSequence	Class DnaSequence encapsulates a DNA sequence.
DnaSequenceList	Class DnaSequenceList provides a list of DnaSequences.
DnaSequenceTree	Class DnaSequenceTree encapsulates a rooted bifurcating tree of DNA sequences.
DrawTree	Class DrawTree is a program that draws a phylogenetic tree.
FitchParsimony	Class FitchParsimony provides the Fitch algorithm for computing the parsimony score of a DnaSequenceTree.
HammingDistance	Class HammingDistance provides an object that computes the Hamming distance between two DnaSequences.
JukesCantorDistance	Class JukesCantorDistance provides an object that computes the Jukes-Cantor distance between two DnaSequences.
LeastSquaresBranchLengths	Class LeastSquaresBranchLengths provides methods for computing least squares branch lengths in a DnaSequenceTree.
MaximumParsimonyBnbHyb	Class MaximumParsimonyBnbHyb provides a hybrid parallel algorithm for maximum parsimony phylogenetic tree construction using branch-and-bound search.
MaximumParsimonyBnbSeq	Class MaximumParsimonyBnbSeq provides a sequential algorithm for maximum parsimony phylogenetic tree construction using branch-and-bound search.
MaximumParsimonyBnbSmp	Class MaximumParsimonyBnbSmp provides an SMP parallel algorithm for maximum parsimony phylogenetic tree construction using branch-and-bound search.
MaximumParsimonyExhSeq	Class MaximumParsimonyExhSeq provides a sequential algorithm for maximum parsimony phylogenetic tree construction using exhaustive search.
MaximumParsimonyResults	Class MaximumParsimonyResults contains the results of a maximum parsimony phylogenetic tree construction algorithm.
PhylogenyParsBnbHyb	Class PhylogenyParsBnbHyb is a hybrid parallel program for maximum parsimony phylogenetic tree construction using branch-and-bound search.
PhylogenyParsBnbSeq	Class PhylogenyParsBnbSeq is a sequential program for maximum parsimony phylogenetic tree construction using branch-and-bound search.
PhylogenyParsBnbSmp	Class PhylogenyParsBnbSmp is an SMP parallel program for maximum parsimony phylogenetic tree construction using branch-and-bound search.
PhylogenyParsExhSeq	Class PhylogenyParsExhSeq is a sequential program for maximum parsimony phylogenetic tree construction using exhaustive search.
Results	Class Results provides a method for reporting the results of a maximum parsimony phylogenetic tree construction program.
TreeDrawing	Class TreeDrawing provides an object that draws a picture of a phylogenetic tree.
Upgma	Class Upgma provides the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm for phylogenetic tree construction.

Exception Summary

Exception	Description
TreeDrawing.SyntaxException	Class TreeDrawing.SyntaxException is an exception thrown if there was a syntax error in a tree string.

Package edu.rit.compbio.phyl Description

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.