Index

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D

Data - Enum in pt.ist.phylolib.cli

Enumerates the available data types with their respective option and class.

Dataset - Class in pt.ist.phylolib.data.dataset

Represents a phylogenetic dataset as profiles.

Dataset(List<Profile>) - Constructor for class pt.ist.phylolib.data.dataset.Dataset

Creates a phylogenetic dataset corresponding to the given profiles.

DATASET - pt.ist.phylolib.cli.Data

DATASET - pt.ist.phylolib.cli.Option

DatasetParser - Class in pt.ist.phylolib.data.dataset

Responsible for parsing phylogenetic datasets from Strings.

DatasetParser() - Constructor for class pt.ist.phylolib.data.dataset.DatasetParser

dissimilarity(double, double, double, int, int) - Method in class pt.ist.phylolib.command.algorithm.gcp.CL

dissimilarity(double, double, double, int, int) - Method in class pt.ist.phylolib.command.algorithm.gcp.GloballyClosestPairs

Calculates the dissimilarity between a given previously existing node and a given node created by joining two existing nodes.

dissimilarity(double, double, double, int, int) - Method in class pt.ist.phylolib.command.algorithm.gcp.SL

dissimilarity(double, double, double, int, int) - Method in class pt.ist.phylolib.command.algorithm.gcp.UPGMA

dissimilarity(double, double, double, int, int) - Method in class pt.ist.phylolib.command.algorithm.gcp.UPGMC

dissimilarity(double, double, double, int, int) - Method in class pt.ist.phylolib.command.algorithm.gcp.WPGMA

dissimilarity(double, double, double, int, int) - Method in class pt.ist.phylolib.command.algorithm.gcp.WPGMC

distance() - Method in class pt.ist.phylolib.data.tree.Edge

distance(int, int) - Method in class pt.ist.phylolib.data.matrix.Matrix

Gets the phylogenetic distance between two given profiles.

distance(Profile, Profile) - Method in class pt.ist.phylolib.command.distance.Distance

Calculates the phylogenetic distance between the two given profiles.

distance(Profile, Profile) - Method in class pt.ist.phylolib.command.distance.GrapeTree

distance(Profile, Profile) - Method in class pt.ist.phylolib.command.distance.Hamming

distance(Profile, Profile) - Method in class pt.ist.phylolib.command.distance.Kimura

Distance - Class in pt.ist.phylolib.command.distance

Responsible for calculating a distance matrix from a phylogenetic dataset.

Distance() - Constructor for class pt.ist.phylolib.command.distance.Distance

DISTANCE - pt.ist.phylolib.cli.Command

DISTANCE - pt.ist.phylolib.cli.Format

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