25 #include "argtable3.h" 35 #ifdef THESE_ARE_COMMENTS 38 #include "hashfunction.h" 41 #include "random_number_gen.h" 57 #endif // of THESE_ARE_COMMENTS 59 #endif //define biomcmc Creates a histogram of a vector, ordered by frequency.
Random number generation, with algorithms from the Gnu Scientific Library (GSL) and motivation from t...
Probability distribution functions and auxiliary mathematical functions from statistical package R...
branch length operations on topologies, including patristic distances
Reads a list of trees in newick format and creates vector of topologies.
binary and multistate parsimony matrices, together with bipartition extraction for MRP ...
General-purpose topology structures created from nexus_tree_struct (and low-level functions) ...
Creation of random topologies and modification of existing ones through branch swapping.
File handling functions and calculation of distances for sequence data in nexus format.
Low-level functions that use only the split bipartitions of topologies – treating them as unrooted u...
find k smallest element in vector
File handling functions for nexus format in general.
Lowest level header file. Header file for lowlevel.c.
distance matrix, that can be used in alignments and trees, and patristic-distance based species dista...
low-level file for gene tree and species tree reconciliation. This file is hidden from user and conta...
gene tree and species tree structures, for reconciliation etc. This is the high-level file with globa...
k-mer handling of DNA sequences, with hash transformation
Low-level functions for reading newick strings.
OPTICS algorithm based on https://github.com/guineri/GOPTICS.
Reads tree files in nexus format and creates a vector of topologies.
Unary/binary operators on arbitrarily-sized bitstrings (strings of zeros and ones) like split biparti...
UPGMA and bioNJ from (onedimensional representation of) distance matrices.
distance calculation between generic objects,without generating full matrix beforehand ...
list of strings (each string is a vector of chars)
double hashing open-address hash table using strings as key – also has distance matrix, that can be used in alignments and trees