biomcmc-lib  0.1
low level library for phylogenetic analysis
lib Directory Reference


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
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 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.