All Classes and Interfaces

Class	Description
Algorithm	Responsible for calculating a phylogenetic tree from a distance matrix.
ArgumentException	Wraps all exceptions derived from command line arguments related issues.
Arguments	Represents the parsed arguments of the program as commands and respective parameters.
Asymmetric	Responsible for parsing distance matrices from and to Strings in an asymmetric format.
CL	Responsible for calculating a phylogenetic tree from a distance matrix using the Complete-Linkage algorithm.
Command	Enumerates the available commands with their respective repeatability and class.
Context	Maintains the shared data context for the program, storing references to the current Dataset, Matrix, and Tree.
Correction	Responsible for correcting a distance matrix into another.
Data	Enumerates the available data types with their respective option and class.
Dataset	Represents a phylogenetic dataset as profiles.
DatasetParser	Responsible for parsing phylogenetic datasets from Strings.
Distance	Responsible for calculating a distance matrix from a phylogenetic dataset.
DistanceScope	The pairwise distance range required by an algorithm or retained by a matrix.
DistanceScope.Bounded	Distances through this finite, non-negative bound are available.
DistanceScope.Complete	Every pairwise distance is available.
Edge	Represents an edge as from and to nodes with a distance between them.
Edmonds	Responsible for calculating a phylogenetic tree from a distance matrix using the Edmonds algorithm.
FASTA	Responsible for parsing phylogenetic datasets from Strings in FASTA format.
File	Represents a file as a data type processor and a path.
Format	Enumerates the available formats with their respective regex.
GloballyClosestPairs	Responsible for calculating a phylogenetic tree from a distance matrix using the Globally Closest Pairs algorithm.
GoeBURST
GoeBURSTFullMST	Builds a complete goeBURST Full MST from an LV/Hamming-style distance matrix.
GrapeTree	Responsible for calculating a distance matrix from a phylogenetic dataset using the GrapeTree distance calculation.
Hamming	Responsible for calculating a distance matrix from a phylogenetic dataset using the Hamming distance calculation.
ICommand<T,R>	Responsible for the common operations of a command.
ICommand.IGetter<T>	Represents the input data getter for a command.
InvalidCommandException	Represents an error derived from the definition of an invalid command in the command line arguments.
InvalidTypeException	Represents an error derived from the definition of an invalid command type in the command line arguments.
IReader<T>	Responsible for the reading of data from files.
IWriter<T>	Responsible for the writing of data into files.
JukesCantor	Responsible for correcting a distance matrix into another using the Jukes-Cantor correction formula.
Kimura	Responsible for calculating a distance matrix from a phylogenetic dataset using the Kimura distance calculation.
LBR	Responsible for optimizing a phylogenetic tree into another using the Local Branch Recrafting algorithm.
Log	Responsible for the logging of information in the program.
Main
Matrix
Matrix.ICorrection	Represents a correction formula for a phylogenetic distance.
Matrix.IDistance	Represents a phylogenetic distance provider between two profiles.
MatrixParser	Responsible for parsing distance matrices from and to Strings.
MatrixStoragePlanner	Selects matrix storage from the available distance scope and a deterministic estimate of complete heap-backed storage.
MatrixStoragePlanner.Storage
MissingInputException	Represents an error derived from the definition of no input for a command in the command line arguments.
MissingTypeException	Represents an error derived from the definition of no type for a command in the command line arguments.
ML	Responsible for parsing phylogenetic datasets from Strings in MLST or MLVA format.
NeighbourJoining	Responsible for calculating a phylogenetic tree from a distance matrix using the Neighbour Joining algorithm.
Newick	Responsible for parsing phylogenetic trees from and to Strings in Newick format.
Nexus	Responsible for parsing phylogenetic trees from and to Strings in Nexus format.
NoCommandException	Represents an error derived from the definition of no command in the command line arguments.
Optimization	Responsible for optimizing a phylogenetic tree into another.
Option	Enumerates the available options with their respective alias and format.
Options	Represents the options of a command as keys and values.
Parameters	Represents the parameters of a command as a type and a set of options.
Profile	Represents a profile as an id and a set of loci.
RepeatedCommandException	Represents an error derived from the definition of an unrepeatable command more than once in the command line arguments.
SaitouNei	Responsible for calculating a phylogenetic tree from a distance matrix using the Neighbour Joining algorithm by Saitou and Nei.
SL	Responsible for calculating a phylogenetic tree from a distance matrix using the Single-Linkage algorithm.
SNP	Responsible for parsing phylogenetic datasets from Strings in SNP format.
StudierKepler	Responsible for calculating a phylogenetic tree from a distance matrix using the Neighbour Joining algorithm by Studier and Kepler.
Symmetric	Responsible for parsing distance matrices from and to Strings in a symmetric format.
SymmetryParser	Responsible for parsing distance matrices from and to Strings.
ThresholdSparseMatrix	A threshold-filtered distance matrix.
Tree	Represents a phylogenetic tree as a set of profiles identified by their ids and the edges that connect those profiles.
TreeParser	Responsible for parsing phylogenetic trees from and to Strings.
Types	Responsible for the use of reflection to search for types of a command or data.
UNJ	Responsible for calculating a phylogenetic tree from a distance matrix using the Unweighted Neighbour Joining algorithm.
UPGMA	Responsible for calculating a phylogenetic tree from a distance matrix using the Unweighted Pair Group Method with Arithmetic-mean algorithm.
UPGMC	Responsible for calculating a phylogenetic tree from a distance matrix using the Unweighted Pair Group Method with Centroid algorithm.
WPGMA	Responsible for calculating a phylogenetic tree from a distance matrix using the Weighted Pair Group Method with Arithmetic-mean algorithm.
WPGMC	Responsible for calculating a phylogenetic tree from a distance matrix using the Weighted Pair Group Method with Centroid algorithm.