Package edu.rit.compbio.phyl

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

See:
          Description

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

Class Summary
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
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:

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

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

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

The following program draws a picture of a phylogenetic tree:

The other classes are used by the above programs.



Copyright © 2005-2012 by Alan Kaminsky. All rights reserved. Send comments to ark­@­cs.rit.edu.