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biomcmc-lib
0.1
low level library for phylogenetic analysis
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__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 |