biomcmclib
0.1
low level library for phylogenetic analysis

__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 arbitrarilysized 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 patristicdistance 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 highlevel file with globally exposed functions/structures 
hashfunctions.h  Collections of hash functions for 32 and 64 bits, including oneliners, murmurhash, and xxhash 
hashtable.h  Double hashing openaddress 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  Kmer 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  Lowlevel functions for reading newick strings 
reconciliation.h  Lowlevel file for gene tree and species tree reconciliation. This file is hidden from user and contains the LCAbased reconciliation distances 
splitset_distances.h  Lowlevel functions that use only the split bipartitions of topologies – treating them as unrooted usually 
topology_common.h  Generalpurpose topology structures created from nexus_tree_struct (and lowlevel 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 