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trees.cpp File Reference

#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include "clustalw.h"
#include "dayhoff.h"

Functions

Boolean transition (sint base1, sint base2)
void tree_gap_delete (void)
void distance_matrix_output (FILE *ofile)
void nj_tree (char **tree_description, FILE *tree)
void compare_tree (char **tree1, char **tree2, sint *hits, sint n)
void print_phylip_tree (char **tree_description, FILE *tree, sint bootstrap)
void print_nexus_tree (char **tree_description, FILE *tree, sint bootstrap)
sint two_way_split (char **tree_description, FILE *tree, sint start_row, sint flag, sint bootstrap)
sint two_way_split_nexus (char **tree_description, FILE *tree, sint start_row, sint flag, sint bootstrap)
void print_tree (char **tree_description, FILE *tree, sint *totals)
static Boolean is_ambiguity (char c)
static void overspill_message (sint overspill, sint total_dists)
void phylogenetic_tree (char *phylip_name, char *clustal_name, char *dist_name, char *nexus_name, char *pim_name)
void fast_nj_tree (char **tree_description, FILE *tree)
void bootstrap_tree (char *phylip_name, char *clustal_name, char *nexus_name)
sint dna_distance_matrix (FILE *tree)
sint prot_distance_matrix (FILE *tree)
void guide_tree (FILE *tree, sint firstseq, sint numseqs)

Variables

sint max_names
double ** tmat
Boolean dnaflag
Boolean tossgaps
Boolean kimura
Boolean output_tree_clustal
Boolean output_tree_phylip
Boolean output_tree_distances
Boolean output_tree_nexus
Boolean output_pim
sint bootstrap_format
Boolean empty
Boolean usemenu
sint nseqs
sint max_aln_length
sint * seqlen_array
char ** seq_array
char ** names
char seqname []
sint gap_pos1
sint gap_pos2
Boolean use_ambiguities
char * amino_acid_codes
static double * av
static double * left_branch
static double * right_branch
static double * save_left_branch
static double * save_right_branch
static sint * boot_totals
static sint * tkill
static sint * boot_positions
static FILE * phylip_phy_tree_file
static FILE * clustal_phy_tree_file
static FILE * distances_phy_tree_file
static FILE * nexus_phy_tree_file
static FILE * pim_file
static Boolean verbose
static char * tree_gaps
static sint first_seq
static sint last_seq
sint boot_ntrials
unsigned sint boot_ran_seed

Function Documentation

void bootstrap_tree char *  phylip_name,
char *  clustal_name,
char *  nexus_name
 

void compare_tree char **  tree1,
char **  tree2,
sint *  hits,
sint  n
 

void distance_matrix_output FILE *  ofile  ) 
 

sint dna_distance_matrix FILE *  tree  ) 
 

void fast_nj_tree char **  tree_description,
FILE *  tree
 

end main cycle*

void guide_tree FILE *  tree,
sint  firstseq,
sint  numseqs
 

static Boolean is_ambiguity char  c  )  [static]
 

void nj_tree char **  tree_description,
FILE *  tree
 

static void overspill_message sint  overspill,
sint  total_dists
[static]
 

void phylogenetic_tree char *  phylip_name,
char *  clustal_name,
char *  dist_name,
char *  nexus_name,
char *  pim_name
 

void print_nexus_tree char **  tree_description,
FILE *  tree,
sint  bootstrap
 

void print_phylip_tree char **  tree_description,
FILE *  tree,
sint  bootstrap
 

void print_tree char **  tree_description,
FILE *  tree,
sint *  totals
 

sint prot_distance_matrix FILE *  tree  ) 
 

Boolean transition sint  base1,
sint  base2
 

void tree_gap_delete void   ) 
 

sint two_way_split char **  tree_description,
FILE *  tree,
sint  start_row,
sint  flag,
sint  bootstrap
 

sint two_way_split_nexus char **  tree_description,
FILE *  tree,
sint  start_row,
sint  flag,
sint  bootstrap
 


Variable Documentation

char* amino_acid_codes
 

double* av [static]
 

sint boot_ntrials
 

sint* boot_positions [static]
 

unsigned sint boot_ran_seed
 

sint* boot_totals [static]
 

sint bootstrap_format
 

FILE* clustal_phy_tree_file [static]
 

FILE* distances_phy_tree_file [static]
 

Boolean dnaflag
 

Boolean empty
 

sint first_seq [static]
 

sint gap_pos1
 

sint gap_pos2
 

Boolean kimura
 

sint last_seq [static]
 

double* left_branch [static]
 

sint max_aln_length
 

sint max_names
 

char** names
 

FILE* nexus_phy_tree_file [static]
 

sint nseqs
 

Boolean output_pim
 

Boolean output_tree_clustal
 

Boolean output_tree_distances
 

Boolean output_tree_nexus
 

Boolean output_tree_phylip
 

FILE* phylip_phy_tree_file [static]
 

FILE* pim_file [static]
 

double * right_branch [static]
 

double* save_left_branch [static]
 

double * save_right_branch [static]
 

char** seq_array
 

sint* seqlen_array
 

char seqname[]
 

sint* tkill [static]
 

double** tmat
 

Boolean tossgaps
 

char* tree_gaps [static]
 

Boolean use_ambiguities
 

Boolean usemenu
 

Boolean verbose [static]
 


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