biomcmc-lib  0.1
low level library for phylogenetic analysis
Data Fields
alignment_struct Struct Reference

Data from alignment file. More...

#include <alignment.h>

Collaboration diagram for alignment_struct:
Collaboration graph

Data Fields

int ntax
int nchar
int npat
char_vector character
 Number of species, sites and patterns according to sequence file.
char_vector taxlabel
 Vector with aligned sequence for each taxon.
char_vector taxshort
 Taxon names from file.
hashtable taxlabel_hash
 Alias (short version) for taxon names that can be used in newick trees.
int n_charset
 Lookup table with taxon names.
int * charset_start
 Number of gene segments (ASSUMPTIONS BLOCK).
int * charset_end
bool is_aligned
 Start and end of each gene segment (from 1...NCHAR) (ASSUMPTIONS ).
int * site_pattern
 FASTA files don't need to be aligned; NEXUS files do.
int * pattern_freq
 pattern, in alignment_struct::character, to which original site belongs.
char * filename
 if sequences are aligned, this is the frequency of each pattern.
int ref_counter
 name of the original file, with extension removed

Detailed Description

Data from alignment file.

The documentation for this struct was generated from the following file: