File List

Here is a list of all documented files with brief descriptions:

__primes_unused.h
_header.h
alignment.h	File handling functions and calculation of distances for sequence data in nexus format
argtable3.h
biomcmc.h	Biomcmc library interface to external programs, specific to super_sptree repo
bipartition.h	Unary/binary operators on arbitrarily-sized bitstrings (strings of zeros and ones) like split bipartitions
char_vector.c	Vector of strings (species names, leaf names, etc.)
char_vector.h	List of strings (each string is a vector of chars)
clustering_goptics.h	OPTICS algorithm based on https://github.com/guineri/GOPTICS
distance_generator.h	Distance calculation between generic objects,without generating full matrix beforehand
distance_matrix.h	Distance matrix, that can be used in alignments and trees, and patristic-distance based species distances
empirical_frequency.c	Histogram of vectors, ordered by frequency. Also calculates MAP (modal) values
empirical_frequency.h	Creates a histogram of a vector, ordered by frequency
genetree.h	Gene tree and species tree structures, for reconciliation etc. This is the high-level file with globally exposed functions/structures
hashfunctions.h	Collections of hash functions for 32 and 64 bits, including one-liners, murmurhash, and xxhash
hashtable.h	Double hashing open-address hash table using strings as key – also has distance matrix, that can be used in alignments and trees
hll.h	HyperLogLog functions, based on code by Ivan Vitjuk https://github.com/ivitjuk/libhll under an ISC License
kmerhash.h	K-mer handling of DNA sequences, with hash transformation
lowlevel.c	Lowest level basic functions, that should be available to all other modules
lowlevel.h	Lowest level header file. Header file for lowlevel.c
newick_space.h	Reads a list of trees in newick format and creates vector of topologies
nexus_common.h	File handling functions for nexus format in general
parsimony.h	Binary and multistate parsimony matrices, together with bipartition extraction for MRP
prob_distribution.h	Probability distribution functions and auxiliary mathematical functions from statistical package R
prob_distribution_aux.h	Auxiliary (low level) functions for prob_distribution.c
quickselect_quantile.h	Find k smallest element in vector
random_number.h	Random number generation, with algorithms from the Gnu Scientific Library (GSL) and motivation from the Scalable Parallel Pseudo Random Number Generators Library (SPRNG)
random_number_aux.h	Variables and structures local to random_number.c (should be opaque to user)
random_number_gen.h
read_newick_trees.h	Low-level functions for reading newick strings
reconciliation.h	Low-level file for gene tree and species tree reconciliation. This file is hidden from user and contains the LCA-based reconciliation distances
splitset_distances.h	Low-level functions that use only the split bipartitions of topologies – treating them as unrooted usually
topology_common.h	General-purpose topology structures created from nexus_tree_struct (and low-level functions)
topology_distance.h	Branch length operations on topologies, including patristic distances
topology_randomise.h	Creation of random topologies and modification of existing ones through branch swapping
topology_space.h	Reads tree files in nexus format and creates a vector of topologies
upgma.h	UPGMA and bioNJ from (onedimensional representation of) distance matrices