lib Directory Reference

Files
file	alignment.h [code]
	File handling functions and calculation of distances for sequence data in nexus format.
file	biomcmc.h [code]
	biomcmc library interface to external programs, specific to super_sptree repo.
file	bipartition.h [code]
	Unary/binary operators on arbitrarily-sized bitstrings (strings of zeros and ones) like split bipartitions.
file	char_vector.c
	vector of strings (species names, leaf names, etc.)
file	char_vector.h [code]
	list of strings (each string is a vector of chars)
file	clustering_goptics.h [code]
	OPTICS algorithm based on https://github.com/guineri/GOPTICS.
file	distance_generator.h [code]
	distance calculation between generic objects,without generating full matrix beforehand
file	distance_matrix.h [code]
	distance matrix, that can be used in alignments and trees, and patristic-distance based species distances
file	empirical_frequency.c
	histogram of vectors, ordered by frequency. Also calculates MAP (modal) values.
file	empirical_frequency.h [code]
	Creates a histogram of a vector, ordered by frequency.
file	genetree.h [code]
	gene tree and species tree structures, for reconciliation etc. This is the high-level file with globally exposed functions/structures.
file	hashfunctions.h [code]
	Collections of hash functions for 32 and 64 bits, including one-liners, murmurhash, and xxhash.
file	hashtable.h [code]
	double hashing open-address hash table using strings as key – also has distance matrix, that can be used in alignments and trees
file	hll.h [code]
	HyperLogLog functions, based on code by Ivan Vitjuk https://github.com/ivitjuk/libhll under an ISC License.
file	kmerhash.h [code]
	k-mer handling of DNA sequences, with hash transformation
file	lowlevel.c
	Lowest level basic functions, that should be available to all other modules.
file	lowlevel.h [code]
	Lowest level header file. Header file for lowlevel.c.
file	newick_space.h [code]
	Reads a list of trees in newick format and creates vector of topologies.
file	nexus_common.h [code]
	File handling functions for nexus format in general.
file	parsimony.h [code]
	binary and multistate parsimony matrices, together with bipartition extraction for MRP
file	prob_distribution.h [code]
	Probability distribution functions and auxiliary mathematical functions from statistical package R.
file	prob_distribution_aux.h [code]
	Auxiliary (low level) functions for prob_distribution.c.
file	quickselect_quantile.h [code]
	find k smallest element in vector
file	random_number.h [code]
	Random number generation, with algorithms from the Gnu Scientific Library (GSL) and motivation from the Scalable Parallel Pseudo Random Number Generators Library (SPRNG).
file	random_number_aux.h [code]
	Variables and structures local to random_number.c (should be opaque to user)
file	read_newick_trees.h [code]
	Low-level functions for reading newick strings.
file	reconciliation.h [code]
	low-level file for gene tree and species tree reconciliation. This file is hidden from user and contains the LCA-based reconciliation distances.
file	splitset_distances.h [code]
	Low-level functions that use only the split bipartitions of topologies – treating them as unrooted usually.
file	topology_common.h [code]
	General-purpose topology structures created from nexus_tree_struct (and low-level functions)
file	topology_distance.h [code]
	branch length operations on topologies, including patristic distances
file	topology_randomise.h [code]
	Creation of random topologies and modification of existing ones through branch swapping.
file	topology_space.h [code]
	Reads tree files in nexus format and creates a vector of topologies.
file	upgma.h [code]
	UPGMA and bioNJ from (onedimensional representation of) distance matrices.