biomcmc-lib  0.1
low level library for phylogenetic analysis
Data Structures
Here are the data structures with brief descriptions:
 Calignment_structData from alignment file
 Cbinary_parsimony_datamatrix_structUsed by matrix representation with parsimony (01 10 11 sequences)
 Cbiomcmc_rng_structRandom number structure (combined Tausworthe algorithm)
 Cbip_hashitem_structKey (bipartition) and value (frequency) pair for hash table of bipartitions
 Cbip_hashtable_structHash table of bipartitions (see hashtable.h for original version, with string keys and integer values)
 Cbipartition_structBit-string representation of splits
 Cchar_vector_structVector of strings (char vectors) of variable length
 Chashtable_item_structKey/value pair for hash table
 Chashtable_structHash table (vector indexed by strings)
 Cnewick_node_structNewick trees have minimal information, unlike topology_struct
 Cnewick_space_structCollection of topologies from tree file. Each topology will have its own char_vector
 Creconciliation_structMapping between gene tree nodes (this) and (external) species tree nodes
 Crng_diaconis_structPersi Diaconis' lagged Fibonacci
 Crng_gfsr4_structGFSR4 implementation from GSL
 Crng_lfib4_structMarsaglia's LFIB4 lagged Fibonacci using addition
 Crng_mt19937_structMT19937-64, the Mersenne Twister for 64 bits
 Crng_mt19937ar_structMT19937, the original Mersenne Twister (for 32 bits); the name "ar" comes from "array"
 Crng_swb_structMarsaglia's Subtract-with-borrow generator
 Crng_tt800_structTt800 (small cousin of MT19937, the Mersenne Twister)
 Ctopol_node_structInformation of a node (binary tree)
 Ctopology_space_structCollection of topologies from tree file. When topologies have no branch lengths we store only unique topologies
 Ctopology_structBinary unrooted topology (rooted at leaf with ID zero)