Index (biojava-phylo 4.2.2 API)

C D E F G I J K M N O P S T V

C

cloneDM(BasicSymmetricalDistanceMatrix) - Static method in class org.biojava.nbio.phylo.ForesterWrapper: Helper function to clone a forester symmetrical DistanceMatrix.
Comparison - Class in org.biojava.nbio.phylo: This class provides static methods for the calculation of the percentage of identity between two aligned sequences.
Comparison() - Constructor for class org.biojava.nbio.phylo.Comparison
convert(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.ForesterWrapper: Convert a BioJava MultipleSequenceAlignment to a forester Msa.

demo - package demo
DemoDistanceTree - Class in demo: This demo contains the CookBook example to create a phylogenetic tree from a multiple sequence alignment (MSA).
DemoDistanceTree() - Constructor for class demo.DemoDistanceTree
dissimilarityScore(MultipleSequenceAlignment<C, D>, SubstitutionMatrix<D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The dissimilarity score is the additive inverse of the similarity score (sum of scores) between two aligned sequences using a substitution model (Substitution Matrix).
DistanceMatrixCalculator - Class in org.biojava.nbio.phylo: The DistanceMatrixCalculator methods generate a DistanceMatrix from a MultipleSequenceAlignment or other indirect distance infomation (RMSD).
distanceTree(BasicSymmetricalDistanceMatrix, TreeConstructorType) - Static method in class org.biojava.nbio.phylo.TreeConstructor
DistanceTreeEvaluator - Class in org.biojava.nbio.phylo: Check the accuracy of a Distance Tree by least squares error (LSE) of the Tree branch lengths and the original Distance Matrix.

evaluate(Phylogeny, DistanceMatrix) - Static method in class org.biojava.nbio.phylo.DistanceTreeEvaluator: Evaluate the goodness of fit of a given tree to the original distance matrix.

ForesterWrapper - Class in org.biojava.nbio.phylo: This class contains wrapper methods for communication between BioJava and forester (e.g, Data Structure conversion).
fractionalDissimilarity(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The fractional dissimilarity (D) is defined as the percentage of sites that differ between two aligned sequences.
fractionalDissimilarityScore(MultipleSequenceAlignment<C, D>, SubstitutionMatrix<D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The fractional dissimilarity score (Ds) is a relative measure of the dissimilarity between two aligned sequences.

getNewickString(Phylogeny, boolean) - Static method in class org.biojava.nbio.phylo.ForesterWrapper: Convert a Phylogenetic tree to its Newick representation, so that it can be exported to an external application.

isGap(char) - Static method in class org.biojava.nbio.phylo.Comparison: Method that determines if a character means a gap in the alignment.

jointSeqStrucDistance(double[][]) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The joint sequence-structure distance (d_SS) is a combination of the sequence-based and the structure-based distances.

kimuraDistance(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The Kimura evolutionary distance (d) is a correction of the fractional dissimilarity (D) specially needed for large evolutionary distances.

name - Variable in enum org.biojava.nbio.phylo.TreeType: Description name of the Tree Type

pamMLdistance(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The PAM (Point Accepted Mutations) distance is a measure of evolutionary distance in protein sequences.
percentageIdentity(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: BioJava implementation for percentage of identity (PID).
PID(String, String) - Static method in class org.biojava.nbio.phylo.Comparison: this is a gapped PID calculation
PID(String, String, int, int) - Static method in class org.biojava.nbio.phylo.Comparison
poissonDistance(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The Poisson (correction) evolutionary distance (d) is a function of the fractional dissimilarity (D), given by:

structuralDistance(double[][], double, double, double) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The structural distance (d_S) uses the structural similarity (or dissimilarity) from a the structural alignment of two protein strutures.

TreeConstructor - Class in org.biojava.nbio.phylo: The TreeConstructor uses the forester library to build different types of phylogenetic trees.
TreeConstructorType - Enum in org.biojava.nbio.phylo: The TreeConstructorType specifies the aligorithm used to construct the tree (clustering algorithm).
TreeType - Enum in org.biojava.nbio.phylo: The TreeType specifies the optimization criteria used to generate the tree.

valueOf(String) - Static method in enum org.biojava.nbio.phylo.TreeConstructorType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.phylo.TreeType: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.biojava.nbio.phylo.TreeConstructorType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.phylo.TreeType: Returns an array containing the constants of this enum type, in the order they are declared.

C D E F G I J K M N O P S T V