Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

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▼NPhyloTree	Contains classes and methods to read, write and manipulate phylogenetic trees.
▼NExtensions	Contains useful extension methods.
CTypeExtensions	Useful extension methods
▼NFormats	Contains classes and methods to read and write phylogenetic trees in multiple formats
CAttribute	Describes an attribute of a node.
CBinaryTree	Contains methods to read and write tree files in binary format.
CBinaryTreeMetadata	Holds metadata information about a file containing trees in binary format.
CNcbiAsnBer	Contains methods to read and write trees in the NCBI ASN.1 binary format. Note: this is a hackish reverse-engineering of the NCBI binary ASN format. A lot of this is derived by assumptions and observations.
CNcbiAsnText	Contains methods to read and write trees in the NCBI ASN.1 text format.
CNEXUS	Contains methods to read and write trees in NEXUS format.
CNWKA	Contains methods to read and write trees in Newick and Newick-with-Attributes (NWKA) format.
▼NSequenceScores
CLikelihoodScores	Contains methods to compute likelihood scores on a tree.
CMissingDataException	Exception that is thrown when not enough data has been supplied.
CParsimonyScore	Contains methods to compute parsimony scores for a tree.
▼NSequenceSimulation	Contains classes and methods that can be used to simulate sequence evolution.
CImmutableRateMatrix	Represents a rate matrix whose values cannot be changed after initialisation.
CIMutableRateMatrix	Represents a rate matrix whose values can be changed after initialisation.
CIndelModel	Represents a model for sequence insertion/deletion.
CInsertion	Represents an insertion event.
CMutableRateMatrix	Represents a rate matrix whose values can be changed after initialisation.
▼CRateMatrix	Represents a rate matrix for a continuous-type Markov chain model. This type cannot be instantiated directly, please use MutableRateMatrix or ImmutableRateMatrix instead, or access the static members for some pre-baked common rate matrices for DNA and protein evolution.
CDNA	Contains rate matrices for DNA sequence evolution.
CProtein	Contains rate matrices for protein sequence evolution.
CSequence	Represents a sequence of characters.
CSequenceSimulation	Contains methods to simulate sequence evolution.
▼NTreeBuilding
CBirthDeathTree	Contains methods to simulate birth-death trees.
CCoalescentTree	Contains methods to simulate coalescent trees.
CDistanceMatrix	Contains methods to compute distance matrices.
CNeighborJoining	Contains methods to compute neighbour-joining trees.
CRandomTree	Contains methods to generate random trees.
CThreadSafeRandom	Represents a thread-safe random number generator.
CUPGMA	Contains methods to compute UPGMA trees.
CAttributeDictionary	Represents the attributes of a node. Attributes Name, Length and Support are always included. See the respective properties for default values.
CTreeCollection	Represents a collection of TreeNode objects. If the full representations of the TreeNode objects reside in memory, this offers the best performance at the expense of memory usage. Alternatively, the trees may be read on demand from a stream in binary format. In this case, accessing any of the trees will require the tree to be parsed. This reduces memory usage, but worsens performance. The internal storage model of the collection is transparent to consumers (except for the difference in performance/memory usage).
CTreeNode	Represents a node in a tree (or a whole tree).