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source: branches/nameserver/GDE/PHYML/utilities.h

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Last change on this file was 4073, checked in by westram, 19 years ago
phyml 2.4.5
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1	/*
2
3	PHYML : a program that computes maximum likelihood phylogenies from
4	DNA or AA homologous sequences
5
6	Copyright (C) Stephane Guindon. Oct 2003 onward
7
8	All parts of the source except where indicated are distributed under
9	the GNU public licence. See http://www.opensource.org for details.
10
11	*/
12
13	#ifndef UTILITIES_H
14	#define UTILITIES_H
15
16
17	#include <stdio.h>
18	#include <stdlib.h>
19	#include <math.h>
20	#include <ctype.h>
21	#include <string.h>
22	#include <time.h>
23
24	#define VERSION "v2.4.5"
25
26	extern int NODE_DEG_MAX;
27	extern int BRENT_ITMAX;
28	extern double BRENT_CGOLD;
29	extern double BRENT_ZEPS;
30	extern double MNBRAK_GOLD;
31	extern double MNBRAK_GLIMIT;
32	extern double MNBRAK_TINY;
33	extern double ALPHA_MIN;
34	extern double ALPHA_MAX;
35	extern double BL_MIN;
36	extern double BL_START;
37	extern double BL_MAX;
38	extern double MIN_DIFF_LK;
39	extern double GOLDEN_R;
40	extern double GOLDEN_C;
41	extern int T_MAX_FILE;
42	extern int T_MAX_LINE;
43	extern int T_MAX_NAME;
44	extern int T_MAX_SEQ;
45	extern int N_MAX_INSERT;
46	extern int N_MAX_OTU;
47	extern double UNLIKELY;
48	extern double NJ_SEUIL;
49	extern int MAX_TOPO_DIST;
50	extern double ROUND_MAX;
51	extern double DIST_MAX;
52	extern int LIM_SCALE;
53	extern double LIM_SCALE_VAL;
54	extern double AROUND_LK;
55	extern double PROP_STEP;
56	extern int T_MAX_ALPHABET;
57	extern double MDBL_MAX;
58	extern double MDBL_MIN;
59	extern int POWELL_ITMAX;
60	extern double LINMIN_TOL;
61
62	#define For(i,n) for(i=0; i<n; i++)
63	#define Fors(i,n,s) for(i=0; i<n; i+=s)
64	#define PointGamma(prob,alpha,beta) PointChi2(prob,2.0(alpha))/(2.0(beta))
65	#define SHFT2(a,b,c) (a)=(b);(b)=(c);
66	#define SHFT3(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
67	#define MAX(a,b) ((a)>(b)?(a):(b))
68	#define MIN(a,b) ((a)<(b)?(a):(b))
69	#define SIGN(a,b) ((b) > 0.0 ? fabs(a) : -fabs(a))
70	#define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
71
72	#define NT 0 /* nucleotides */
73	#define AA 1 /* amino acids */
74
75	#define ACGT 0 /* A,G,G,T encoding */
76	#define RY 1 /* R,Y encoding */
77
78
79	#define NODE_DEG_MAX 50
80	#define BRENT_ITMAX 100
81	#define BRENT_CGOLD 0.3819660
82	#define BRENT_ZEPS 1.e-10
83	#define MNBRAK_GOLD 1.618034
84	#define MNBRAK_GLIMIT 100.0
85	#define MNBRAK_TINY 1.e-20
86	#define ALPHA_MIN 0.04
87	#define ALPHA_MAX 100
88	#define BL_MIN 1.e-10
89	#define BL_START 1.e-03
90	#define BL_MAX 1.e+05
91	#define MIN_DIFF_LK 1.e-06
92	#define GOLDEN_R 0.61803399
93	#define GOLDEN_C (1.0-GOLDEN_R)
94	#define T_MAX_FILE 200
95	#define T_MAX_LINE 100000
96	#define T_MAX_NAME 100
97	#define T_MAX_SEQ 1000000
98	#define N_MAX_INSERT 20
99	#define N_MAX_OTU 4000
100	#define UNLIKELY -1.e10
101	#define NJ_SEUIL 0.1
102	#define ROUND_MAX 100
103	#define DIST_MAX 2.00
104	#define AROUND_LK 50.0
105	#define PROP_STEP 1.0
106	#define T_MAX_ALPHABET 100
107	#define MDBL_MIN 2.225074E-308
108	#define MDBL_MAX 1.797693E+308
109	#define POWELL_ITMAX 200
110	#define LINMIN_TOL 2.0E-04
111	#define LIM_SCALE 3
112	#define LIM_SCALE_VAL 1.E-50
113	/* LIM_SCALE = 300; */
114	/* LIM_SCALE_VAL = 1.E-500; */
115
116
117	/*********************************************************/
118
119	typedef struct __Node {
120	struct __Node *v; / table of pointers to neighbor nodes. Dimension = 2 x n_otu - 3 */
121	struct __Node **bip_node; / three lists of pointer to tip nodes. One list for each direction */
122	struct __Edge *b; / table of pointers to neighbor branches */
123	char **bip_name; / three lists of tip node names. One list for each direction */
124	int bip_size; / Size of each of the three lists from bip_node */
125	double l; / lengths of the (three or one) branches connected to one internal node */
126	int num; /* node number */
127	char name; / taxon name (if exists) */
128	int tax; /* tax = 1 -> external node, else -> internal node */
129	int check_branch; /* check_branch=1 is the corresponding branch is labelled with '' /
130	double score; / score used in BIONJ to determine the best pair of nodes to agglomerate */
131	}node;
132
133
134	/*********************************************************/
135
136	typedef struct __Edge {
137	/*
138	syntax : (node) [edge]
139	(left_1) . .(right_1)
140	\ (left) (right) /
141	\._____________./
142	/ [b_fcus] \
143	/ \
144	(left_2) . .(right_2)
145
146	*/
147
148	struct __Node left,rght; /* node on the left/right side of the edge */
149	int l_r,r_l,l_v1,l_v2,r_v1,r_v2;
150	/* these are directions (i.e., 0, 1 or 2): */
151	/* l_r (left to right) -> left[b_fcus->l_r] = right */
152	/* r_l (right to left) -> right[b_fcus->r_l] = left */
153	/* l_v1 (left node to first node != from right) -> left[b_fcus->l_v1] = left_1 */
154	/* l_v2 (left node to secnd node != from right) -> left[b_fcus->l_v2] = left_2 */
155	/* r_v1 (right node to first node != from left) -> right[b_fcus->r_v1] = right_1 */
156	/* r_v2 (right node to secnd node != from left) -> right[b_fcus->r_v2] = right_2 */
157
158	int num; /* branch number */
159	double l; /* branch length */
160	double best_l; /* best branch length found so far */
161	double l_old; /* old branch length */
162
163	int bip_score; /* score of the bipartition generated by the corresponding edge
164	bip_score = 1 iif the branch is fond in both trees to be compared,
165	bip_score = 0 otherwise. */
166	double nj_score; /* score of the agglomeration that generated that branch in BIONJ */
167	double diff_lk; /* difference of likelihood between the current topological
168	configuration at this branch and the best alternative one */
169
170	int get_p_lk_left; /* 1 if the likelihood of the subtree on the left has to be computed */
171	int get_p_lk_rght; /* 1 if the likelihood of the subtree on the right has to be computed */
172	int ud_p_lk_left; /* 1 if the likelihood of the subtree on the left is up to date */
173	int ud_p_lk_rght; /* 1 if the likelihood of the subtree on the right is up to date */
174	double site_dlk; /* derivative of the likelihood (deprecated) */
175	double site_d2lk; /* 2nd derivative of the likelihood (deprecated) */
176	double site_dlk_rr; / derivative of the likelihood conditional on the current relative rate */
177	double site_d2lk_rr; / 2nd derivative of the likelihood conditional on the current relative rate */
178	double *p_lk_left,p_lk_rght; / likelihoods of the subtree on the left and
179	right side (for each site and each relative rate category) */
180	double site_p_lk_rght, site_p_lk_left; /* deprecated */
181	double *Pij_rr,dPij_rr,*d2Pij_rr; / matrix of change probabilities and its first and secnd derivates */
182
183	double ql; / ql[0], ql[1], ql[2] give the likelihood of the three topological
184	configurations around that branch */
185	int best_conf; /* best topological configuration :
186	((left_1,left_2),right_1,right_2) or
187	((left_1,right_2),right_1,left_2) or
188	((left_1,right_1),right_1,left_2) */
189
190	int num_st_left; /* number of the subtree on the left side */
191	int num_st_rght; /* number of the subtree on the right side */
192
193
194	/* Below are the likelihood scaling factors (used in functions
195	`Get_All_Partial_Lk_Scale' in lk.c */
196	int scale_left;
197	int scale_rght;
198	double site_sum_scale_f_left;
199	double site_sum_scale_f_rght;
200	double site_scale_f_left;
201	double site_scale_f_rght;
202	double *sum_scale_f_left;
203	double *sum_scale_f_rght;
204
205
206	double bootval; /* bootstrap value (if exists) */
207	}edge;
208
209	/*********************************************************/
210
211	typedef struct __Arbre {
212	struct __Node root; / root node */
213	struct __Node *noeud; / array of nodes that defines the tree topology */
214	struct __Edge *t_edges; / array of edges */
215	struct __Arbre old_tree; / old copy of the tree */
216	struct __Arbre best_tree; / best tree found so far */
217	struct __Model mod; / substitution model */
218	struct __AllSeq data; / sequences */
219	struct __Option input; / input parameters */
220	struct __Matrix mat; / pairwise distance matrix */
221
222	int has_bip; /*if has_bip=1, then the structure to compare
223	tree topologies is allocated, has_bip=0 otherwise */
224	double min_diff_lk; /* min_diff_lk is the minimum taken among the 2n-3
225	diff_lk values */
226
227	int both_sides; /* both_sides=1 -> a pre-order and a post-order tree
228	traversals are required to compute the likelihood
229	of every subtree in the phylogeny*/
230	int n_otu; /* number of taxa */
231
232	int curr_site; /* current site of the alignment to be processed */
233	int curr_catg; /* current class of the discrete gamma rate distribution */
234	double best_loglk; /* highest value of the loglikelihood found so far */
235
236	double tot_loglk; /* loglikelihood */
237	double tot_loglk_sorted; / used to compute tot_loglk by adding sorted terms to minimize CPU errors */
238	double tot_dloglk; / first derivative of the likelihood with respect to
239	branch lengths */
240	double tot_d2loglk; / second derivative of the likelihood with respect to
241	branch lengths */
242	double site_lk; / vector of likelihoods at individual sites */
243
244	double *log_site_lk_cat; / loglikelihood at individual sites and for each class of rate*/
245
246	double unconstraint_lk; /* unconstrained (or multinomial) likelihood */
247
248	int n_swap; /* number of NNIs performed */
249	int n_pattern; /* number of distinct site patterns */
250	int has_branch_lengths; /* =1 iff input tree displays branch lengths */
251	int print_boot_val; /* if print_boot_val=1, the bootstrap values are printed */
252	}arbre;
253
254
255	/*********************************************************/
256
257	typedef struct __Seq {
258	char name; / sequence name */
259	int len; /* sequence length */
260	char state; / sequence itself */
261	}seq;
262
263	/*********************************************************/
264
265
266	typedef struct __AllSeq {
267	seq *c_seq; / compressed sequences */
268	int invar; / 1 -> states are identical, 0 states vary */
269	double wght; / # of each site in c_seq */
270	int n_otu; /* number of taxa */
271	int clean_len; /* uncrunched sequences lenghts without gaps */
272	int crunch_len; /* crunched sequences lengths */
273	double b_frq; / observed state frequencies */
274	int init_len; /* length of the uncompressed sequences */
275	int ambigu; / ambigu[i]=1 is one or more of the sequences at site
276	i display an ambiguous character */
277	int sitepatt; / this array maps the position of the patterns in the
278	compressed alignment to the positions in the uncompressed
279	one */
280	}allseq;
281
282	/*********************************************************/
283
284	typedef struct __Matrix { /* mostly used in BIONJ */
285	double P,Q,*dist; / observed proportions of transition, transverion and distances
286	between pairs of sequences */
287	arbre tree; / tree... */
288	int on_off; / on_off[i]=1 if column/line i corresponds to a node that has not
289	been agglomerated yet */
290	int n_otu; /* number of taxa */
291	char *name; / sequence names */
292	int r; /* number of nodes that have not been agglomerated yet */
293	struct __Node *tip_node; / array of pointer to the leaves of the tree */
294	int curr_int; /* used in the NJ/BIONJ algorithms */
295	int method; /* if method=1->NJ method is used, BIONJ otherwise */
296	}matrix;
297
298	/*********************************************************/
299
300	typedef struct __Model {
301	int whichmodel;
302	/*
303	1 => JC69
304	2 => K2P
305	3 => F81
306	4 => HKY85
307	5 => F84
308	6 => TN93
309	7 => GTR
310	11 => Dayhoff
311	12 => JTT
312	13 => MtREV
313	*/
314	int ns; /* number of states (4 for ADN, 20 for AA) */
315	double pi; / states frequencies */
316	int datatype; /* 0->DNA, 1->AA */
317
318	/* ADN parameters */
319	double kappa; /* transition/transversion rate */
320	double lambda; /* parameter used to define the ts/tv ratios in the F84 and TN93 models */
321	double alpha; /* gamma shapa parameter */
322	double r_proba; / probabilities of the substitution rates defined by the discrete gamma distribution */
323	double rr; / substitution rates defined by the discrete gamma distribution */
324	int n_catg; /* number of categories in the discrete gamma distribution */
325	double pinvar; /* proportion of invariable sites */
326	int invar; /* =1 iff the substitution model takes into account invariable sites */
327
328	/* Below are 'old' values of some substitution parameters (see the comments above) */
329	double alpha_old;
330	double kappa_old;
331	double lambda_old;
332	double pinvar_old;
333
334	char custom_mod_string; / string of characters used to define custom
335	models of substitution */
336	double *rr_param; / table of pointers to relative rate parameters of the GTR or custom model */
337	double rr_param_values; / relative rate parameters of the GTR or custom model */
338	int *rr_param_num; / each line of this 2d table gives a serie of equal relative rate parameter number */
339	/* A<->C : number 0 */
340	/* A<->G : number 1 */
341	/* A<->T : number 2 */
342	/* C<->G : number 3 */
343	/* C<->T : number 4 */
344	/* G<->T : number 5 */
345	/* For example, [0][2][3]
346	[1]
347	[4][5]
348	corresponds to the model 010022, i.e.,
349	(A<->C = A<->T = C<->T) != (A<->G) != (C<->T = G<->T)
350	*/
351	int n_rr_param_per_cat; / [3][1][2] for the previous example */
352	int n_diff_rr_param; /* number of different relative substitution rates in the custom model */
353
354	int update_eigen; /* update_eigen=1-> eigen values/vectors need to be updated */
355
356	double **Pij_rr; / matrix of change probabilities */
357	double **dPij_rr; / first derivative of the change probabilities with respect to branch length */
358	double **d2Pij_rr; / second derivative of the change probabilities with respect to branch length */
359
360
361	int seq_len; /* sequence length */
362	/* AA parameters */
363	/* see PMat_Empirical in models.c for AA algorithm explanation */
364	double mat_Q; / 20x20 amino-acids substitution rates matrix */
365	double mat_Vr; / 20x20 right eigenvectors of mat_Q */
366	double mat_Vi; / 20x20 inverse matrix of mat_Vr */
367	double vct_ev; / eigen values */
368	double mr; /* mean rate = branch length/time interval */
369	/* mr = -sum(i)(vct_pi[i].mat_Q[ii]) */
370	double vct_eDmr; / diagonal terms of a 20x20 diagonal matrix */
371	/* term n = exp(nth eigenvalue of mat_Q / mr) */
372	int stepsize; /* stepsize=1 for nucleotide models, 3 for codon models */
373	int n_otu; /* number of taxa */
374	struct __Optimiz s_opt; / pointer to parameters to optimize */
375	int bootstrap; /* bootstrap values are computed if bootstrap > 0.
376	The value give the number of replicates */
377	double user_b_freq; / user-defined nucleotide frequencies */
378
379
380	}model;
381
382	/*********************************************************/
383
384	typedef struct __Option { /* mostly used in 'options.c' */
385	char seqfile; / sequence file name */
386	char modelname; / name of the model */
387	struct __Model mod; / substitution model */
388	int interleaved; /* interleaved or sequential sequence file format ? */
389	int inputtree; /* =1 iff a user input tree is used as input */
390	struct __Arbre tree; / pointer to the current tree */
391	char inputtreefile; / input tree file name */
392	FILE fp_seq; / pointer to the sequence file */
393	FILE fp_input_tree; / pointer to the input tree file */
394	FILE fp_boot_tree; / pointer to the bootstrap tree file */
395	FILE fp_boot_stats; / pointer to the statistics file */
396	int print_boot_trees; /* =1 if the bootstrapped trees are printed in output */
397	char phyml_stat_file; / name of the statistics file */
398	char phyml_tree_file; / name of the tree file */
399	char phyml_lk_file; / name of the file in which the likelihood of the model is written */
400	int phyml_stat_file_open_mode; /* opening file mode for statistics file */
401	int phyml_tree_file_open_mode; /* opening file mode for tree file */
402	int n_data_sets; /* number of data sets to be analysed */
403	int n_trees; /* number of trees */
404	int seq_len; /* sequence length */
405	int n_data_set_asked; /* number of bootstrap replicates */
406	struct __Seq *data; / pointer to the uncompressed sequences */
407	struct __AllSeq alldata; / pointer to the compressed sequences */
408	char nt_or_cd; / nucleotide or codon data ? (not used) */
409	}option;
410
411	/*********************************************************/
412
413	typedef struct __Optimiz { /* parameters to be optimised (mostly used in 'optimiz.c') */
414	int print; /* =1 -> verbose mode */
415
416	int opt_alpha; /* =1 -> the gamma shape parameter is optimised */
417	int opt_kappa; /* =1 -> the ts/tv ratio parameter is optimised */
418	int opt_lambda; /* =1 -> the F84\|TN93 model specific parameter is optimised */
419	int opt_pinvar; /* =1 -> the proportion of invariants is optimised */
420	int opt_bfreq; /* =1 -> the nucleotide frequencies are optimised */
421	int opt_rr_param; /* =1 -> the relative rate parameters of the GTR or the customn model are optimised */
422	int opt_free_param; /* if opt_topo=0 and opt_free_param=1 -> the numerical parameters of the
423	model are optimised. if opt_topo=0 and opt_free_param=0 -> no parameter is
424	optimised */
425	int opt_bl; /* =1 -> the branch lengths are optimised */
426	int opt_topo; /* =1 -> the tree topology is optimised */
427	double init_lk; /* initial loglikelihood value */
428	int n_it_max; /* maximum bnumber of iteration during an optimisation step */
429	int last_opt; /* =1 -> the numerical parameters are optimised further while the
430	tree topology remains fixed */
431	}optimiz;
432
433	/*********************************************************/
434
435	typedef struct __Qmat{
436	double *u_mat; / right eigen vectors */
437	double *v_mat; / left eigen vectors = inv(u_mat) */
438	double root_vct; / eigen values */
439	double q; / instantaneous rate matrix */
440	}qmat;
441
442	/*********************************************************/
443
444	double bico(int n,int k);
445	double factln(int n);
446	double gammln(double xx);
447	double Pbinom(int N,int ni,double p);
448	void Plim_Binom(double pH0,int N,double pinf,double psup);
449	double LnGamma(double alpha);
450	double IncompleteGamma(double x,double alpha,double ln_gamma_alpha);
451	double PointChi2(double prob,double v);
452	double PointNormal(double prob);
453	int DiscreteGamma(double freqK[],double rK[],double alfa,double beta,int K,int median);
454	arbre Read_Tree(char s_tree);
455	void Make_All_Edges_Light(node a,node d);
456	void Make_All_Edges_Lk(node a,node d,arbre *tree);
457	void R_rtree(char s_tree,node pere,arbre tree,int n_int,int *n_ext);
458	void Clean_Multifurcation(char **subtrees,int current_deg,int end_deg);
459	char *Sub_Trees(char tree,int *degree);
460	int Next_Par(char *s,int pos);
461	char Write_Tree(arbre tree);
462	void R_wtree(node pere,node fils,char s_tree,arbre tree);
463	void Init_Tree(arbre *tree);
464	void Make_Edge_Light(node a,node d);
465	void Init_Edge_Light(edge *b);
466	void Make_Edge_Dirs(edge b,node a,node *d);
467	void Make_Edge_Lk(node a,node d,arbre *tree);
468	void Make_Node_Light(node *n);
469	void Init_Node_Light(node *n);
470	void Make_Node_Lk(node *n);
471	seq *Get_Seq(option input,int rw);
472	seq *Read_Seq_Sequential(FILE in,int *n_otu);
473	seq *Read_Seq_Interleaved(FILE in,int *n_otu);
474	int Read_One_Line_Seq(seq **data,int num_otu,FILE in);
475	void Uppercase(char *ch);
476	allseq Compact_Seq(seq data,option input);
477	allseq Compact_CSeq(allseq data,model *mod);
478	void Get_Base_Freqs(allseq *data);
479	void Get_AA_Freqs(allseq *data);
480	arbre Read_Tree_File(FILE fp_input_tree);
481	void Init_Tree_Edges(node a,node d,arbre tree,int cur);
482	void Exit(char *message);
483	void *mCalloc(int nb,size_t size);
484	void mRealloc(void p,int nb,size_t size);
485	arbre *Make_Light_Tree_Struct(int n_otu);
486	int Sort_Double_Decrease(const void a,const void b);
487	void qksort(double *A,int ilo,int ihi);
488	void Print_Site(allseq alldata,int num,int n_otu,char sep,int stepsize);
489	void Print_Seq(seq **data,int n_otu);
490	void Print_CSeq(FILE fp,allseq alldata);
491	void Order_Tree_Seq(arbre tree,seq *data);
492	void Order_Tree_CSeq(arbre tree,allseq data);
493	matrix *Make_Mat(int n_otu);
494	void Init_Mat(matrix mat,allseq data);
495	arbre Make_Tree(allseq data);
496	void Print_Dist(matrix *mat);
497	void Print_Node(node a,node d,arbre *tree);
498	void Share_Lk_Struct(arbre t_full,arbre t_empt);
499	void Init_Constant();
500	void Print_Mat(matrix *mat);
501	int Sort_Edges_Diff_Lk(arbre tree,edge *sorted_edges,int n_elem);
502	void NNI(arbre tree,edge b_fcus,int do_swap);
503	void Swap(node a,node b,node c,node d,arbre *tree);
504	void Update_All_Partial_Lk(edge b_fcus,arbre tree);
505	void Update_SubTree_Partial_Lk(edge b_fcus,node a,node d,arbre tree);
506	double Update_Lk_At_Given_Edge(edge b_fcus,arbre tree);
507	void Update_PMat_At_Given_Edge(edge b_fcus,arbre tree);
508	allseq Make_Seq(int n_otu,int len,char *sp_names);
509	allseq Copy_CData(allseq ori,model *mod);
510	optimiz *Alloc_Optimiz();
511	void Init_Optimiz(optimiz *s_opt);
512	int Filexists(char *filename);
513	FILE Openfile(char filename,int mode);
514	void Print_Fp_Out(FILE fp_out,time_t t_beg,time_t t_end,arbre tree,option *input,int n_data_set);
515	void Print_Fp_Out_Lines(FILE fp_out,time_t t_beg,time_t t_end,arbre tree,option *input,int n_data_set);
516	void Alloc_All_P_Lk(arbre *tree);
517	matrix K2P_dist(allseq data,double g_shape);
518	matrix JC69_Dist(allseq data,model *mod);
519	matrix Hamming_Dist(allseq data,model *mod);
520	int Is_Ambigu(char *state,int datatype,int stepsize);
521	void Check_Ambiguities(allseq *data,int datatype,int stepsize);
522	int Assign_State(char *c,int datatype,int stepsize);
523	void Bootstrap(arbre *tree);
524	void Update_BrLen_Invar(arbre *tree);
525	void Getstring_Stdin(char *file_name);
526	void Print_Freq(arbre *tree);
527	double Num_Derivatives_One_Param(double(func)(arbre tree),arbre tree,double f0,double param,double stepsize,double *err,int precise);
528	void Num_Derivative_Several_Param(arbre tree,double param,int n_param,double stepsize,double(func)(arbre tree),double *derivatives);
529	int Compare_Two_States(char state1,char state2,int state_size);
530	void Copy_One_State(char from,char to,int state_size);
531	model *Make_Model_Basic();
532	void Make_Model_Complete(model *mod);
533	model Copy_Model(model ori);
534	void Set_Defaults_Input(option *input);
535	void Set_Defaults_Model(model *mod);
536	void Set_Defaults_Optimiz(optimiz *s_opt);
537	void Copy_Optimiz(optimiz ori,optimiz cpy);
538	void Get_Bip(node a,node d,arbre *tree);
539	void Alloc_Bip(arbre *tree);
540	int Sort_Double_Increase(const void a,const void b);
541	int Sort_String(const void a,const void b);
542	void Compare_Bip(arbre tree1,arbre tree2);
543	void Test_Multiple_Data_Set_Format(option *input);
544	int Are_Compatible(char statea,char stateb,int stepsize,int datatype);
545	void Hide_Ambiguities(allseq *data);
546	void Print_Site_Lk(arbre tree, FILE fp);
547	#endif
548
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