Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · b9d1db11
--- a/debian/changelog
+++ b/debian/changelog
+t-coffee (12.00.7fb08c2-1) unstable; urgency=medium
+
+  * New upstream version
+
+ -- Andreas Tille <tille@debian.org>  Mon, 17 Dec 2018 15:02:59 +0100
+
 t-coffee (11.00.8cbe486-8) unstable; urgency=medium

  * Team upload.

--- a/debian/patches/clustalw2.patch
+++ b/debian/patches/clustalw2.patch
@@ -7,7 +7,7 @@ Last-Update:  Fri, 16 Dec 2016 15:00:58 +0100

 --- a/t_coffee_source/perl_header_lib.h
 +++ b/t_coffee_source/perl_header_lib.h
-@@ -5177,7 +5177,7 @@ po_store(\"./src/$pg\");\n	  }\n	else\n
+@@ -5379,7 +5379,7 @@ po_store(\"./src/$pg\");\n	  }\n	else\n
 h_command (\"make $arguments sap\");\n	    &check_\
 cp ($pg, \"$BIN\");\n	    repo_store($pg);\n	  }\n\
       }\n    \n    #\n    # CLUSTALW2 module\n    \
@@ -16,33 +16,33 @@ Last-Update:  Fri, 16 Dec 2016 15:00:58 +0100
 ush_command(\"./configure\");\n	&flush_command(\"m\
 ake $arguments\");\n	&check_cp (\"./src/$pg\", \"$\
 BIN\");\n	repo_store(\"./src/$pg\");\n      }\n\n \
-@@ -5534,16 +5534,16 @@ trike/index.html\";\n$PG{\"strike\"}{\"l
- \n$PG{\"strike\"}{\"source\"}=\"http://www.tcoffee\
- .org/Projects/strike/strike_v1.2.tar.bz2\";\n$PG{\\
- "strike\"}{\"mode\"}=\"tcoffee,expresso\";\n$PG{\"\
-strike\"}{\"version\"}=\"1.2\";\n$PG{\"clustalw2\"\
-}{\"4_TCOFFEE\"}=\"CLUSTALW2\";\n$PG{\"clustalw2\"\
-+strike\"}{\"version\"}=\"1.2\";\n$PG{\"clustalw\"\
-+}{\"4_TCOFFEE\"}=\"CLUSTALW2\";\n$PG{\"clustalw\"\
- }{\"type\"}=\"sequence_multiple_aligner\";\n$PG{\"\
-clustalw2\"}{\"ADDRESS\"}=\"http://www.clustal.org\
-\";\n$PG{\"clustalw2\"}{\"language\"}=\"C++\";\n$P\
-G{\"clustalw2\"}{\"language2\"}=\"CXX\";\n$PG{\"cl\
-+clustalw\"}{\"ADDRESS\"}=\"http://www.clustal.org\
-+\";\n$PG{\"clustalw\"}{\"language\"}=\"C++\";\n$P\
-+G{\"clustalw\"}{\"language2\"}=\"CXX\";\n$PG{\"cl\
- ustalw2\"}{\"source\"}=\"http://www.clustal.org/do\
- wnload/2.0.10/clustalw-2.0.10-src.tar.gz\";\n$PG{\\
-"clustalw2\"}{\"mode\"}=\"mcoffee,rcoffee\";\n$PG{\
-\"clustalw2\"}{\"version\"}=\"2.0.10\";\n$PG{\"clu\
-+"clustalw\"}{\"mode\"}=\"mcoffee,rcoffee\";\n$PG{\
-+\"clustalw\"}{\"version\"}=\"2.0.10\";\n$PG{\"clu\
- stalw\"}{\"4_TCOFFEE\"}=\"CLUSTALW\";\n$PG{\"clust\
- alw\"}{\"type\"}=\"sequence_multiple_aligner\";\n$\
- PG{\"clustalw\"}{\"ADDRESS\"}=\"http://www.clustal\
+@@ -5732,15 +5732,15 @@ nguage\"}=\"C++\";\n$PG{\"strike\"}{\"la
+ w.tcoffee.org/Projects/strike/strike_v1.2.tar.bz2\\
+ ";\n$PG{\"strike\"}{\"mode\"}=\"tcoffee,expresso\"\
+ ;\n$PG{\"strike\"}{\"version\"}=\"1.2\";\n$PG{\"cl\
+-ustalw2\"}{\"4_TCOFFEE\"}=\"CLUSTALW2\";\n$PG{\"cl\
+-ustalw2\"}{\"type\"}=\"sequence_multiple_aligner\"\
+-;\n$PG{\"clustalw2\"}{\"ADDRESS\"}=\"http://www.cl\
+-ustal.org\";\n$PG{\"clustalw2\"}{\"language\"}=\"C\
+-++\";\n$PG{\"clustalw2\"}{\"language2\"}=\"CXX\";\\
+-n$PG{\"clustalw2\"}{\"source\"}=\"http://www.clust\
+ustalw\"}{\"4_TCOFFEE\"}=\"CLUSTALW2\";\n$PG{\"cl\
+ustalw\"}{\"type\"}=\"sequence_multiple_aligner\"\
+;\n$PG{\"clustalw\"}{\"ADDRESS\"}=\"http://www.cl\
+ustal.org\";\n$PG{\"clustalw\"}{\"language\"}=\"C\
+++\";\n$PG{\"clustalw\"}{\"language2\"}=\"CXX\";\\
+n$PG{\"clustalw\"}{\"source\"}=\"http://www.clust\
+ al.org/download/2.0.10/clustalw-2.0.10-src.tar.gz\\
+-";\n$PG{\"clustalw2\"}{\"mode\"}=\"mcoffee,rcoffee\
+-\";\n$PG{\"clustalw2\"}{\"version\"}=\"2.0.10\";\n\
+";\n$PG{\"clustalw\"}{\"mode\"}=\"mcoffee,rcoffee\
+\";\n$PG{\"clustalw\"}{\"version\"}=\"2.0.10\";\n\
+ $PG{\"clustalw\"}{\"4_TCOFFEE\"}=\"CLUSTALW\";\n$P\
+ G{\"clustalw\"}{\"type\"}=\"sequence_multiple_alig\
+ ner\";\n$PG{\"clustalw\"}{\"ADDRESS\"}=\"http://ww\
 --- a/t_coffee_source/util_lib/util_constraints_list.c
 +++ b/t_coffee_source/util_lib/util_constraints_list.c
-@@ -5677,7 +5677,7 @@ char *** produce_method_file ( char *met
+@@ -5887,7 +5887,7 @@ char *** produce_method_file ( char *met
 	sprintf (list[n][1], "%s", vtmpnam(NULL));
 	n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
 	fprintf ( fp, "EXECUTABLE profile_pair\n");
@@ -51,7 +51,7 @@ Last-Update:  Fri, 16 Dec 2016 15:00:58 +0100
 	fprintf ( fp, "ALN_MODE   pairwise\n");
 	fprintf ( fp, "OUT_MODE   fL\n");
 	fprintf ( fp, "IN_FLAG    -profile1=\n");
-@@ -5917,7 +5917,7 @@ char *** produce_method_file ( char *met
+@@ -6162,7 +6162,7 @@ char *** produce_method_file ( char *met
 	sprintf (list[n][1], "%s", vtmpnam(NULL));
 	n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
 	fprintf ( fp, "DOC: clustalw [%s]\n", CLUSTALW2_ADDRESS);
@@ -60,7 +60,7 @@ Last-Update:  Fri, 16 Dec 2016 15:00:58 +0100
 	fprintf ( fp, "ALN_MODE   pairwise\n");
 	fprintf ( fp, "OUT_MODE   aln\n");
 	fprintf ( fp, "IN_FLAG    %sINFILE=\n",CWF);
-@@ -5932,7 +5932,7 @@ char *** produce_method_file ( char *met
+@@ -6177,7 +6177,7 @@ char *** produce_method_file ( char *met
 	sprintf (list[n][1], "%s", vtmpnam(NULL));
 	n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
 	fprintf ( fp, "DOC clustalw[%s]\n", CLUSTALW2_ADDRESS);
@@ -69,7 +69,7 @@ Last-Update:  Fri, 16 Dec 2016 15:00:58 +0100
 	fprintf ( fp, "ALN_MODE   multiple\n");
 	fprintf ( fp, "OUT_MODE   aln\n");
 	fprintf ( fp, "IN_FLAG    %sINFILE=\n",CWF);
-@@ -5947,7 +5947,7 @@ char *** produce_method_file ( char *met
+@@ -6192,7 +6192,7 @@ char *** produce_method_file ( char *met
 	sprintf (list[n][1], "%s", vtmpnam(NULL));
 	n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
 	fprintf ( fp, "DOC: clustalw [%s]\n", CLUSTALW_ADDRESS);
@@ -78,7 +78,7 @@ Last-Update:  Fri, 16 Dec 2016 15:00:58 +0100
 	fprintf ( fp, "ALN_MODE   pairwise\n");
 	fprintf ( fp, "OUT_MODE   aln\n");
 	fprintf ( fp, "IN_FLAG    %sINFILE=\n", CWF);
-@@ -5962,7 +5962,7 @@ char *** produce_method_file ( char *met
+@@ -6207,7 +6207,7 @@ char *** produce_method_file ( char *met
 	sprintf (list[n][1], "%s", vtmpnam(NULL));
 	n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
 	fprintf ( fp, "DOC clustalw[%s]\n", CLUSTALW_ADDRESS);
@@ -100,7 +100,7 @@ Last-Update:  Fri, 16 Dec 2016 15:00:58 +0100
 #define CLUSTALO_ADDRESS "http://www.clustal.org/omega/"
 --- a/install
 +++ b/install
-@@ -798,7 +798,7 @@ sub install_source_package
+@@ -799,7 +799,7 @@ sub install_source_package
     #
     # CLUSTALW2 module
     #
@@ -109,7 +109,7 @@ Last-Update:  Fri, 16 Dec 2016 15:00:58 +0100
       {
 	&flush_command("./configure");
 	&flush_command("make $arguments");
-@@ -1577,22 +1577,14 @@ $PG{"strike"}{"language2"}="CXX";
+@@ -1565,22 +1565,14 @@ $PG{"strike"}{"language2"}="CXX";
 $PG{"strike"}{"source"}="http://www.tcoffee.org/Projects/strike/strike_v1.2.tar.bz2";
 $PG{"strike"}{"mode"}="tcoffee,expresso";
 $PG{"strike"}{"version"}="1.2";
@@ -139,7 +139,7 @@ Last-Update:  Fri, 16 Dec 2016 15:00:58 +0100
 $PG{"dialign-t"}{"ADDRESS"}="http://dialign-tx.gobics.de/";
 --- a/t_coffee_source/programmes_define.h
 +++ b/t_coffee_source/programmes_define.h
-@@ -60,7 +60,7 @@
+@@ -61,7 +61,7 @@
 #define STRIKE_source "http://www.tcoffee.org/Projects/strike/strike_v1.2.tar.bz2"
 #define STRIKE_mode "tcoffee,expresso"
 #define STRIKE_version "1.2"
@@ -150,7 +150,7 @@ Last-Update:  Fri, 16 Dec 2016 15:00:58 +0100
 #define CLUSTALW2_language "C++"
 --- a/tclinkdb.txt
 +++ b/tclinkdb.txt
-@@ -25,14 +25,14 @@ PG strike source		http://www.tcoffee.org
+@@ -26,23 +26,14 @@ PG strike source		http://www.tcoffee.org
 PG strike mode			tcoffee,expresso
 PG strike version		1.2
      
@@ -162,14 +162,20 @@ Last-Update:  Fri, 16 Dec 2016 15:00:58 +0100
 -PG clustalw2 source		http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz
 -PG clustalw2 mode		mcoffee,rcoffee
 -PG clustalw2 version		2.0.10
+-
+-PG clustalw 4_TCOFFEE		CLUSTALW
 +PG clustalw 4_TCOFFEE		CLUSTALW2
-+PG clustalw type		sequence_multiple_aligner		
-+PG clustalw ADDRESS		http://www.clustal.org
+ PG clustalw type		sequence_multiple_aligner		
+ PG clustalw ADDRESS		http://www.clustal.org
+-PG clustalw language		C
+-PG clustalw language2		C
+-PG clustalw source		http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw1.82.UNIX.tar.gz
 +PG clustalw language		C++
 +PG clustalw language2		CXX
 +PG clustalw source		http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz
-+PG clustalw mode		mcoffee,rcoffee
+ PG clustalw mode		mcoffee,rcoffee
+-PG clustalw version		1.82
 +PG clustalw version		2.0.10
 
- PG clustalw 4_TCOFFEE		CLUSTALW
- PG clustalw type		sequence_multiple_aligner		
+ PG dialign-t 4_TCOFFEE		DIALIGNT		
+ PG dialign-t type		sequence_multiple_aligner		
--- a/debian/patches/debug.patch
+++ b/debian/patches/debug.patch
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Fri, 28 Sep 2018 14:24:07 +0200
-Bug-Debian: https://bugs.debian.org/909530
-Description: Try to find the problem that causes coredump
-
--- a/t_coffee_source/util_lib/util_constraints_list.c
-+++ b/t_coffee_source/util_lib/util_constraints_list.c
-@@ -1335,6 +1335,7 @@ Constraint_list *  undump_constraint_lis
- 	int *entry, b, c, e, tot;
- 	FILE *fp;
- 
-+fprintf (stderr, "\nDEBUG %s(%i):  file = %s", __FILE__, __LINE__, file);
- 	if (!CL || !CL->residue_index)return CL;
- 	entry=(int*)vcalloc ( CL->entry_len+1, sizeof (int));
- 	fp=vfopen (file, "r");
-@@ -2147,25 +2148,29 @@ Constraint_list* fork_read_n_constraint_
- 		int pid;
- 		ns++;
- 		pid=vvfork (NULL);
-+fprintf (stderr, "\nDEBUG %s(%i):  ns = %i, pid = %i, a = %i, n_list = %i", __FILE__, __LINE__, ns, pid, a, n_list);
- 		if ( pid==0)
- 		{
- 			int in;
- 			initiate_vtmpnam (NULL);
- 			CL->local_stderr=vfopen("/dev/null", "w");
- 			in=CL->ne;
-+fprintf (stderr, "\nDEBUG %s(%i):  in = %i, fname[a] = %s, in_mode = %s, mem_mode = %s, weight_mode = %s", __FILE__, __LINE__, in, fname[a], in_mode, mem_mode, weight_mode);
- 			CL=read_constraint_list (CL, fname[a], in_mode, mem_mode,weight_mode);
- 			if (CL->ne>in)dump_constraint_list(CL,tmp_list[a], "w");
-+fprintf (stderr, "\nDEBUG %s(%i): before exit  in = %i", __FILE__, __LINE__, in);
- 			myexit (EXIT_SUCCESS);
- 		}
- 		else
- 		{
- 			//set_pid (pid);
-			fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s", fname[a], ns);
-+			fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s (ns=%i)", fname[a], ns);
- 			proclist[pid]=a;
- 			if (ns>=nproc)
- 			{
- 				b=proclist[vwait(NULL)];
- 				fprintf (local_stderr, "\n\txxx Retrieved %s",fname[a]);
-+fprintf (stderr, "\nDEBUG %s(%i): ns = %i, nproc = %i, tmp_list_b_%i_ = %s", __FILE__, __LINE__, ns, nproc, b, tmp_list[b]);
- 				if (tmp_list[b] && check_file_exists (tmp_list[b]))
- 				{
- 					CL=undump_constraint_list(CL,tmp_list[b]);
-@@ -2178,14 +2183,18 @@ Constraint_list* fork_read_n_constraint_
- 	while (ns)
- 	{
- 		int pid2;
-+fprintf (stderr, "\nDEBUG %s(%i): before vwait(): pid2 = %i", __FILE__, __LINE__, pid2);
- 		pid2=vwait(NULL);
-+fprintf (stderr, "\nDEBUG %s(%i): after vwait()", __FILE__, __LINE__);
- 		a=proclist[pid2];
- 		fprintf (local_stderr, "\n\txxx Retrieved %s",fname[a]);
-+fprintf (stderr, "\nDEBUG %s(%i): n_list = %i, nproc = %i, tmp_list_a_%i_ = %s", __FILE__, __LINE__, ns, n_list, a, tmp_list[a]);
- 		if (tmp_list[a] && check_file_exists (tmp_list[a]))
- 		{
- 			CL=undump_constraint_list (CL,tmp_list[a]);
- 		}
- 		ns--;
-+fprintf (stderr, "\nDEBUG %s(%i):  ns = %i", __FILE__, __LINE__, ns);
- 	}
- 	fprintf ( local_stderr, "\n\n\tAll Methods Retrieved\n");
- 
-@@ -2216,11 +2225,20 @@ Constraint_list* read_constraint_list(Co
- 	Sequence *SL=NULL, *TS=NULL;
- 	int a;
- 	Constraint_list *SUBCL=NULL;
-	static char *read_mode;
-+	/*static char *read_mode;*/
-+	static char read_mode[STRING];
- 	char *fname;
- 
-+fprintf (stderr, "\nDEBUG %s(%i):  in_fname = %s, in_mode = %s, mem_mode = %s, weight_mode = %s", __FILE__, __LINE__, in_fname, in_mode, mem_mode, weight_mode);
- 	fname=in_fname;
-	if ( !read_mode)read_mode=(char*)vcalloc ( STRING, sizeof (char));
-+	/*if ( !read_mode)read_mode=(char*)vcalloc ( STRING, sizeof (char));*/
-+
-+if (read_mode)
-+fprintf (stderr, "\nDEBUG %s(%i):  read_mode = %s, STRING = %i", __FILE__, __LINE__, read_mode, STRING);
-+else
-+fprintf (stderr, "\nDEBUG %s(%i):  STRING = %s, fname = %s", __FILE__, __LINE__, STRING, fname);
-+sprintf ( read_mode, "structure");
-+fprintf (stderr, "\nDEBUG %s(%i):  read_mode = %s, fname[0] = %c", __FILE__, __LINE__, STRING, fname[0]);
- 
- 	if ( is_lib_list (in_fname))sprintf ( read_mode, "lib_list");
- 	else if ( in_mode)sprintf (read_mode, "%s", in_mode);
--- a/t_coffee_source/util_lib/util.c
-+++ b/t_coffee_source/util_lib/util.c
-@@ -4348,7 +4348,9 @@ pid_t vwait (pid_t *p)
- 
- 
-   p2=wait(&rv); 
-+fprintf (stderr, "\nDEBUG %s(%i): before check_process() p2 = %i", __FILE__, __LINE__, p2);
-   if (p2!=-1)rv=check_process("forked::T-Coffee", p2, rv,handle_failure);
-+fprintf (stderr, "\nDEBUG %s(%i): after check_process() p2 = %i", __FILE__, __LINE__, p2);
-   if ( p) p[0]=rv;
- 
-   return p2;
-@@ -4957,7 +4959,9 @@ int  set_unique_dir_4_tcoffee (char *dir
- void myexit (int signal)
- {
- 
-+fprintf (stderr, "\nDEBUG %s(%i): in myexit() signal = %i", __FILE__, __LINE__, signal);
-   if (clean_exit_started==1)return; //protects processes while they are doing a clean exit
-+fprintf (stderr, "\nDEBUG %s(%i): in myexit() signal = %i", __FILE__, __LINE__, signal);
-   global_exit_signal=signal;
-   exit (global_exit_signal); //ONLY BARE EXIT!!!!!!!!!!!!!!
- }
-@@ -5589,6 +5593,7 @@ void dump_tcoffee(char *target, char *na
-   char *out_list;
- 
-   
-+fprintf (stderr, "\nDEBUG %s(%i): dump_tcoffee() target = %s, nature = %s, pid = %i, ppid = %i", __FILE__, __LINE__, target, nature, getpid(), getppid());
- 
-   if ((fp=fopen (target, "w")))
-     {
-@@ -5663,6 +5668,8 @@ void dump_error_file()
-   FILE *fp;
- 
- 
-+fprintf (stderr, "\nDEBUG %s(%i): dump_error_file() pid = %i, ppid = %i", __FILE__, __LINE__, getpid(), getppid());
-+
-   sprintf ( target, "%s",getenv("ERRORFILE_4_TCOFFEE"));
-   if (strstr (target, "NO"));
-   else
-@@ -8962,6 +8969,9 @@ void clean_exit ()
-   Tmpname *start;
-   int debug;
- 
-+fprintf (stderr, "\nDEBUG %s(%i): clean_exit() pid = %i, ppid = %i", __FILE__, __LINE__, getpid(), getppid());
-+/* https://stackoverflow.com/questions/26256996/who-called-atexit */
-+/* abort(); */
-   clean_exit_started=1;//prevent new locks
-   start=tmpname;
-   //1-start killing all the children
-@@ -8979,6 +8989,7 @@ void clean_exit ()
- 
-   if (is_rootpid())
-     {
-+fprintf (stderr, "\nDEBUG %s(%i): clean_exit() / is_rootpid()=true: pid = %i, ppid = %i", __FILE__, __LINE__, getpid(), getppid());
- 
-       kill_child_pid(getpid());
-       if (has_error_lock())
-@@ -8988,6 +8999,7 @@ void clean_exit ()
- 	  warning_msg (stderr);
- 	  e=lock (getpid(), LERROR, LREAD, NULL);
- 
-+fprintf (stderr, "\nDEBUG %s(%i): clean_exit() / has_error_lock()=true: e = '%s'\n", __FILE__, __LINE__, e);
- 
- 
- 	  //explicit the most common error messages
--- a/t_coffee_source/t_coffee_lib/t_coffee.c
-+++ b/t_coffee_source/t_coffee_lib/t_coffee.c
-@@ -4762,7 +4762,9 @@ get_cl_param(\
- 		     }
- 		   else
- 		     {
-+fprintf (stderr, "\nDEBUG %s(%i): before read_n_constraint_list(): infile = %s", __FILE__, __LINE__, infile);
- 		     CL=read_n_constraint_list (list_file,n_list,NULL, mem_mode,weight,type, le, CL, seq_source);
-+fprintf (stderr, "\nDEBUG %s(%i): after read_n_constraint_list(): infile = %s", __FILE__, __LINE__, infile);
- 		     }
- 		 }
- 	       if ( CL->M)clean_aln=0;
--- a/debian/patches/fix_missing_return.patch
+++ b/debian/patches/fix_missing_return.patch
-Author: Liubov Chuprikova <chuprikovalv@gmail.com>
-Last-Update: Sun, 21 Oct 2018 11:00:25 +0200
-Bug-Debian: https://bugs.debian.org/909530
-Description: Add missing return that causes coredump
-
-
--- a/t_coffee_source/util_lib/util.c
-+++ b/t_coffee_source/util_lib/util.c
-@@ -1846,6 +1846,7 @@
-     sprintf(name, "%s", cwd);
-   else
-     perror("getcwd() error");
-+  return name;
- }
- 
- 
--- a/debian/patches/gcc-7.patch
+++ b/debian/patches/gcc-7.patch
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Sun, 27 Aug 2017 15:36:36 +0200
-Bug-Debian: https://bugs.debian.org/853677
-Description: Fix some string assignments
-
--- a/t_coffee_source/util_lib/aln_convertion_util.c
-+++ b/t_coffee_source/util_lib/aln_convertion_util.c
-@@ -5513,7 +5513,7 @@ Sequence * swap_header ( Sequence *S, Se
- 
- 	     list=string2list (H->seq_comment[n]);
- 	     if ( list==NULL || atoi(list[0])==1)continue;
-	     S->seq_comment[a]='\0';
-+	     S->seq_comment[a]="";
- 	     sprintf (S->name[a], "%s%s%s",H->name[n], list[1], list[2]);
- 	     vfree ( S->seq_comment[a]);S->seq_comment[a]=(char*)vcalloc ( strlen (H->seq_comment[n])+1, sizeof (char));
- 	     for (b=3; b< atoi(list[0]); b++)S->seq_comment[a]=strcat (S->seq_comment[a], list[b]);
--- a/t_coffee_source/util_lib/util.c
-+++ b/t_coffee_source/util_lib/util.c
-@@ -5301,7 +5301,7 @@ char* store_string_variable (char *name,
- 		  val_array[a]=(char*)vrealloc (val_array[a], strlen (v)+1);
- 		  sprintf (val_array[a],"%s",v);
- 		}
-	      else val_array[a]='\0';
-+	      else val_array[a]="";
- 	      return v;
- 	    }
- 	}
--- a/debian/patches/mayhem.patch
+++ b/debian/patches/mayhem.patch
@@ -10,7 +10,7 @@ Description: Fix Mayhem issue

 --- a/t_coffee_source/util_lib/util.c
 +++ b/t_coffee_source/util_lib/util.c
-@@ -4642,7 +4642,8 @@ char *get_home_4_tcoffee ()
+@@ -5275,7 +5275,8 @@ char *get_home_4_tcoffee ()
     }
   else
     {
@@ -20,7 +20,7 @@ Description: Fix Mayhem issue
     }
 
 
-@@ -7717,6 +7718,10 @@ int my_mkdir ( char *dir_in)
+@@ -8726,6 +8727,10 @@ int my_mkdir ( char *dir_in)
   static char *home = getenv ("HOME");
   static mode_t oldmask = umask(0);
   int change_umask = 0;

--- a/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch
+++ b/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch
@@ -7,9 +7,9 @@ Description: Cope with renaming of scripts in ncbi-blast++
      s/legacy_blast\.pl/legacy_blast/
      s/blastpgp\.pl/blastpgp/

--- T-COFFEE_distribution_Version_11.00.8cbe486.orig/t_coffee_source/programmes_define.h
-+++ T-COFFEE_distribution_Version_11.00.8cbe486/t_coffee_source/programmes_define.h
-@@ -309,7 +309,7 @@
+--- a/t_coffee_source/programmes_define.h
+++ b/t_coffee_source/programmes_define.h
+@@ -336,7 +336,7 @@
 #define EBIWUBLASTc_source "empty"
 #define EBIWUBLASTc_update_action "never"
 #define EBIWUBLASTc_mode "psicoffee,expresso,accurate"
@@ -18,8 +18,8 @@ Description: Cope with renaming of scripts in ncbi-blast++
 #define EBIBLASTPGPc_type "protein_homology_predictor"
 #define EBIBLASTPGPc_ADDRESS "built_in"
 #define EBIBLASTPGPc_ADDRESS2 "http://www.ebi.ac.uk/Tools/webservices/services/blastpgp"
-@@ -326,7 +326,7 @@
- #define blastall_source "empty"
+@@ -353,7 +353,7 @@
+ #define blastall_source "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz"
 #define blastall_update_action "never"
 #define blastall_mode "psicoffee,expresso,3dcoffee"
 -#define NCBIBLAST_4_TCOFFEE "legacy_blast.pl"
@@ -27,9 +27,9 @@ Description: Cope with renaming of scripts in ncbi-blast++
 #define NCBIBLAST_type "protein_homology_predictor"
 #define NCBIBLAST_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"
 #define NCBIBLAST_language "C"
--- T-COFFEE_distribution_Version_11.00.8cbe486.orig/install
-+++ T-COFFEE_distribution_Version_11.00.8cbe486/install
-@@ -1826,15 +1826,15 @@
+--- a/install
+++ b/install
+@@ -1840,15 +1840,15 @@ $PG{"wublast.pl"}{"language2"}="Perl";
 $PG{"wublast.pl"}{"source"}="empty";
 $PG{"wublast.pl"}{"update_action"}="never";
 $PG{"wublast.pl"}{"mode"}="psicoffee,expresso,accurate";
@@ -54,8 +54,8 @@ Description: Cope with renaming of scripts in ncbi-blast++
 $PG{"blastall"}{"4_TCOFFEE"}="blastall";
 $PG{"blastall"}{"type"}="protein_homology_predictor";
 $PG{"blastall"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
-@@ -1843,14 +1843,14 @@
- $PG{"blastall"}{"source"}="empty";
+@@ -1857,14 +1857,14 @@ $PG{"blastall"}{"language2"}="C";
+ $PG{"blastall"}{"source"}="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz";
 $PG{"blastall"}{"update_action"}="never";
 $PG{"blastall"}{"mode"}="psicoffee,expresso,3dcoffee";
 -$PG{"legacy_blast.pl"}{"4_TCOFFEE"}="NCBIBLAST";
@@ -63,7 +63,7 @@ Description: Cope with renaming of scripts in ncbi-blast++
 -$PG{"legacy_blast.pl"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
 -$PG{"legacy_blast.pl"}{"language"}="C";
 -$PG{"legacy_blast.pl"}{"language2"}="C";
-$PG{"legacy_blast.pl"}{"source"}="empty";
+-$PG{"legacy_blast.pl"}{"source"}="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz";
 -$PG{"legacy_blast.pl"}{"update_action"}="never";
 -$PG{"legacy_blast.pl"}{"mode"}="psicoffee,expresso,3dcoffee";
 +$PG{"legacy_blast"}{"4_TCOFFEE"}="NCBIBLAST";
@@ -71,15 +71,15 @@ Description: Cope with renaming of scripts in ncbi-blast++
 +$PG{"legacy_blast"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
 +$PG{"legacy_blast"}{"language"}="C";
 +$PG{"legacy_blast"}{"language2"}="C";
-+$PG{"legacy_blast"}{"source"}="empty";
+$PG{"legacy_blast"}{"source"}="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz";
 +$PG{"legacy_blast"}{"update_action"}="never";
 +$PG{"legacy_blast"}{"mode"}="psicoffee,expresso,3dcoffee";
 $PG{"SOAP::Lite"}{"4_TCOFFEE"}="SOAPLITE";
 $PG{"SOAP::Lite"}{"type"}="library";
 $PG{"SOAP::Lite"}{"ADDRESS"}="http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile.PL";
--- T-COFFEE_distribution_Version_11.00.8cbe486.orig/t_coffee_source/perl_header_lib.h
-+++ T-COFFEE_distribution_Version_11.00.8cbe486/t_coffee_source/perl_header_lib.h
-@@ -31,7 +31,7 @@
+--- a/t_coffee_source/perl_header_lib.h
+++ b/t_coffee_source/perl_header_lib.h
+@@ -31,7 +31,7 @@ tc_generic_method.pl","rnapdb2protpdb.pl
 _method.tc_method","clustalw_method.tc_method","ex\
 tract_from_pdb","install.pl","clean_cache.pl","nat\
 ure_protocol.pl","mocca","dalilite.pl","wublast.pl\
@@ -87,127 +87,72 @@ Description: Cope with renaming of scripts in ncbi-blast++
 +","blastpgp","ncbiblast_lwp.pl","wublast_lwp.pl\
 ","RNAplfold2tclib.pl","fasta_seq2RNAplfold_templa\
 tefile.pl","fasta_seq2hmmtop_fasta.pl","fasta_seq2\
- consan_aln.pl","clustalw_aln2fasta_aln.pl","msf_al\
-@@ -1493,7 +1493,7 @@
- urn 0;}\n      }\n    else\n      {\n	$r=`which $p\
-  2>/dev/null`;\n	if ($r eq \"\"){$r=0;}\n	else {$r\
- =1;}\n\n	if ($r==0 && is_blast_package ($p)){retur\
-n pg_is_installed (\"legacy_blast.pl\");}\n	else {\
-+n pg_is_installed (\"legacy_blast\");}\n	else {\
- return $r;}\n      }\n  }\n\nsub is_blast_package\\
- n  {\n    my $p=shift;\n    if ( $p=~/blastp/){ret\
- urn 1;}\n    elsif ($p=~/blastall/){return 1;}\n  \
-@@ -2077,7 +2077,7 @@
- ) {`mv $outfile.xml $outfile`;}\n	      }\n	    el\
- se\n	      {\n		if ($cl_method eq \"psiblast\"){$c\
- l_method =\"blastp -j5\";}\n\n		$command=\"t_coffe\
-e -other_pg blastpgp.pl --email $EMAIL $infile -d \
-+e -other_pg blastpgp --email $EMAIL $infile -d \
- $db --outfile $outfile -p $cl_method --mode PSI-Bl\
- ast>/dev/null 2>$error_log\";\n		&safe_system ( $c\
- ommand);\n\n		if (-e \"$outfile.xml\") {`mv $outfi\
-@@ -2130,20 +2130,20 @@
- R\"};\n		$cl_db=\"$x$db\";\n	      }\n	    else\n	\
-       {\n		$cl_db=$db;\n	      }\n\n        ##\n		\
- ## BLAST+ provide different binaries names and CLI\
- options\n		## Use the 'legacy_blast.pl' to keep c\
-+ options\n		## Use the 'legacy_blast' to keep c\
- ompatibility with old blast commands\n		##\n		$pat\
-h=`which legacy_blast.pl 2>/dev/null`;  \n		$path=\
-+h=`which legacy_blast 2>/dev/null`;  \n		$path=\
- `dirname $path`; \n		chomp($path);\n	    if ($meth\
- od eq \"blastp\")\n	      {\n		&check_configuratio\
-n(\"legacy_blast.pl\");\n		$command=\"legacy_blast\
-.pl blastpgp --path $path -d $cl_db -i $infile -o \
-+n(\"legacy_blast\");\n		$command=\"legacy_blast\
-+ blastpgp --path $path -d $cl_db -i $infile -o \
- $outfile -m7 -j1\";\n	      }\n	    elsif ($method\
-  eq \"psiblast\")\n	      {\n		&check_configuratio\
-n(\"legacy_blast.pl\");\n		$command=\"legacy_blast\
-+n(\"legacy_blast\");\n		$command=\"legacy_blast\
- .pl blastpgp --path $path -d $cl_db -i $infile -o \
- $outfile -m7 -j5\";\n	      }\n	    elsif ($method\
-  eq \"blastn\")\n	      {\n		&check_configuration(\
-\"legacy_blast.pl\");\n		$command=\"legacy_blast.p\
-+\"legacy_blast\");\n		$command=\"legacy_blast.p\
- l blastall --path $path -p blastn -d $cl_db -i $in\
- file -o $outfile -m7 -W6\";\n	      }\n	    &safe_\
- system ($command);\n	  }\n	else\n	  {\n\n	    myex\
-@@ -5801,16 +5801,16 @@
- erl\";\n$PG{\"wublast.pl\"}{\"source\"}=\"empty\";\
- \n$PG{\"wublast.pl\"}{\"update_action\"}=\"never\"\
- ;\n$PG{\"wublast.pl\"}{\"mode\"}=\"psicoffee,expre\
-sso,accurate\";\n$PG{\"blastpgp.pl\"}{\"4_TCOFFEE\\
-"}=\"EBIBLASTPGPc\";\n$PG{\"blastpgp.pl\"}{\"type\\
-+sso,accurate\";\n$PG{\"blastpgp\"}{\"4_TCOFFEE\\
-+"}=\"EBIBLASTPGPc\";\n$PG{\"blastpgp\"}{\"type\\
- "}=\"protein_homology_predictor\";\n$PG{\"blastpgp\
- .pl\"}{\"ADDRESS\"}=\"built_in\";\n$PG{\"blastpgp.\
- pl\"}{\"ADDRESS2\"}=\"http://www.ebi.ac.uk/Tools/w\
-ebservices/services/blastpgp\";\n$PG{\"blastpgp.pl\
-\"}{\"language\"}=\"Perl\";\n$PG{\"blastpgp.pl\"}{\
-\"language2\"}=\"Perl\";\n$PG{\"blastpgp.pl\"}{\"s\
-ource\"}=\"empty\";\n$PG{\"blastpgp.pl\"}{\"update\
-_action\"}=\"never\";\n$PG{\"blastpgp.pl\"}{\"mode\
-+ebservices/services/blastpgp\";\n$PG{\"blastpgp\
-+\"}{\"language\"}=\"Perl\";\n$PG{\"blastpgp\"}{\
-+\"language2\"}=\"Perl\";\n$PG{\"blastpgp\"}{\"s\
-+ource\"}=\"empty\";\n$PG{\"blastpgp\"}{\"update\
-+_action\"}=\"never\";\n$PG{\"blastpgp\"}{\"mode\
- \"}=\"psicoffee,expresso,accurate\";\n$PG{\"blasta\
- ll\"}{\"4_TCOFFEE\"}=\"blastall\";\n$PG{\"blastall\
- \"}{\"type\"}=\"protein_homology_predictor\";\n$PG\
-@@ -5820,14 +5820,14 @@
- 2\"}=\"C\";\n$PG{\"blastall\"}{\"source\"}=\"empty\
- \";\n$PG{\"blastall\"}{\"update_action\"}=\"never\\
- ";\n$PG{\"blastall\"}{\"mode\"}=\"psicoffee,expres\
-so,3dcoffee\";\n$PG{\"legacy_blast.pl\"}{\"4_TCOFF\
-EE\"}=\"NCBIBLAST\";\n$PG{\"legacy_blast.pl\"}{\"t\
-+so,3dcoffee\";\n$PG{\"legacy_blast\"}{\"4_TCOFF\
-+EE\"}=\"NCBIBLAST\";\n$PG{\"legacy_blast\"}{\"t\
- ype\"}=\"protein_homology_predictor\";\n$PG{\"lega\
- cy_blast.pl\"}{\"ADDRESS\"}=\"ftp://ftp.ncbi.nih.g\
- ov/blast/executables/LATEST\";\n$PG{\"legacy_blast\
-.pl\"}{\"language\"}=\"C\";\n$PG{\"legacy_blast.pl\
-\"}{\"language2\"}=\"C\";\n$PG{\"legacy_blast.pl\"\
-}{\"source\"}=\"empty\";\n$PG{\"legacy_blast.pl\"}\
-+.pl\"}{\"language\"}=\"C\";\n$PG{\"legacy_blast\
-+\"}{\"language2\"}=\"C\";\n$PG{\"legacy_blast\"\
-+}{\"source\"}=\"empty\";\n$PG{\"legacy_blast\"}\
- {\"update_action\"}=\"never\";\n$PG{\"legacy_blast\
- .pl\"}{\"mode\"}=\"psicoffee,expresso,3dcoffee\";\\
- n$PG{\"SOAP::Lite\"}{\"4_TCOFFEE\"}=\"SOAPLITE\";\\
-@@ -6654,23 +6654,23 @@
-           :      : show SOAP messages being interc\
- hanged\n\nSynchronous job:\n\n  The results/errors\
-  are returned as soon as the job is finished.\n  U\
-sage: blastpgp.pl --email <your@email> [options...\
-+sage: blastpgp --email <your@email> [options...\
- ] seqfile\n  Returns: saves the results to disk\n\\
- nAsynchronous job:\n\n  Use this if you want to re\
- trieve the results at a later time. The results\n \
-  are stored for up to 24 hours.\n  The asynchronou\
- s submission mode is recommended when users are su\
- bmitting\n  batch jobs or large database searches\\
-n  Usage: blastpgp.pl --email <your@email> --async\
-+n  Usage: blastpgp --email <your@email> --async\
-  [options...] seqFile\n  Returns: jobid\n\n  Use t\
- he jobid to query for the status of the job.\n  Us\
-age: blastpgp.pl --status --jobid <jobId>\n  Retur\
-+age: blastpgp --status --jobid <jobId>\n  Retur\
- ns: string indicating the status of the job\n    D\
- ONE - job has finished\n    RUNNING - job is runni\
- ng\n    NOT_FOUND - job cannot be found\n    ERROR\
-  - the jobs has encountered an error\n\n  When don\
- e, use the jobid to retrieve the results of the jo\
-b.\n  Usage: blastpgp.pl --polljob --jobid <jobId>\
-+b.\n  Usage: blastpgp --polljob --jobid <jobId>\
-  [--outfile <fileName>]\n  Returns: saves the resu\
- lts to disk\nEOF\n;\n}\n","\n=head1 NAME\n\nncbibl\
- ast_lwp.pl\n\n=head1 DESCRIPTION\n\nNCBI BLAST (RE\
--- T-COFFEE_distribution_Version_11.00.8cbe486.orig/tclinkdb.txt
-+++ T-COFFEE_distribution_Version_11.00.8cbe486/tclinkdb.txt
-@@ -309,15 +309,15 @@
+ consan_aln.pl","clustalw_aln2fasta_aln.pl","seq2na\
+@@ -1558,7 +1558,7 @@ rl -M$p -e 1\")==$EXIT_SUCCESS){return 1
+ {return 0;}\n      }\n    else\n      {\n	$r=`whic\
+ h $p 2>/dev/null`;\n	if ($r eq \"\"){$r=0;}\n	else\
+  {$r=1;}\n\n	if ($r==0 && is_blast_package ($p)){r\
+-eturn pg_is_installed (\"legacy_blast.pl\");}\n	el\
+eturn pg_is_installed (\"legacy_blast\");}\n	el\
+ se {return $r;}\n      }\n  }\n\nsub is_blast_pack\
+ age\n  {\n    my $p=shift;\n    if ( $p=~/blastp/)\
+ {return 1;}\n    elsif ($p=~/blastall/){return 1;}\
+@@ -2230,19 +2230,19 @@ L\")\n	  {\n	    if ($ENV{\"BLAST_DB_DIR
+ n        ##\n		## BLAST+ provide different binarie\
+ s names and CLI options\n		## Use the 'legacy_blas\
+ t.pl' to keep compatibility with old blast command\
+-s\n		##\n		$path=`which legacy_blast.pl 2>/dev/nul\
+s\n		##\n		$path=`which legacy_blast 2>/dev/nul\
+ l`;  \n		$path=`dirname $path`; \n		chomp($path);\\
+ n	    if ($method eq \"blastp\"){\n			&check_confi\
+-guration(\"legacy_blast.pl\");\n			$command=\"lega\
+-cy_blast.pl blastpgp --path $path -d $cl_db -i $in\
+guration(\"legacy_blast\");\n			$command=\"lega\
+cy_blast blastpgp --path $path -d $cl_db -i $in\
+ file -o $outfile -m7 -j1\";\n	    }\n	    elsif ($\
+ method eq \"psiblast\")\n	      {\n		&check_config\
+-uration(\"legacy_blast.pl\");\n		$command=\"legacy\
+-_blast.pl blastpgp --path $path -d $cl_db -i $infi\
+uration(\"legacy_blast\");\n		$command=\"legacy\
+_blast blastpgp --path $path -d $cl_db -i $infi\
+ le -o $outfile -m7 -j5\";\n	      }\n	    elsif ($\
+ method eq \"blastn\")\n	      {\n		&check_configur\
+-ation(\"legacy_blast.pl\");\n		$command=\"legacy_b\
+-last.pl blastall --path $path -p blastn -d $cl_db \
+ation(\"legacy_blast\");\n		$command=\"legacy_b\
+last blastall --path $path -p blastn -d $cl_db \
+ -i $infile -o $outfile -m7 -W6\";\n	      }\n	    \
+ &safe_system ($command);\n	  }\n	else\n	  {\n\n	  \
+   myexit(add_error (EXIT_FAILURE,$$,$$,getppid(), \
+@@ -6046,17 +6046,17 @@ tp.ncbi.nlm.nih.gov/blast/executables/bl
+ /ncbi-blast-2.6.0+-src.tar.gz\";\n$PG{\"blastall\"\
+ }{\"update_action\"}=\"never\";\n$PG{\"blastall\"}\
+ {\"mode\"}=\"psicoffee,expresso,3dcoffee\";\n$PG{\\
+-"legacy_blast.pl\"}{\"4_TCOFFEE\"}=\"NCBIBLAST\";\\
+-n$PG{\"legacy_blast.pl\"}{\"type\"}=\"protein_homo\
+-logy_predictor\";\n$PG{\"legacy_blast.pl\"}{\"ADDR\
+"legacy_blast\"}{\"4_TCOFFEE\"}=\"NCBIBLAST\";\\
+n$PG{\"legacy_blast\"}{\"type\"}=\"protein_homo\
+logy_predictor\";\n$PG{\"legacy_blast\"}{\"ADDR\
+ ESS\"}=\"ftp://ftp.ncbi.nih.gov/blast/executables/\
+-LATEST\";\n$PG{\"legacy_blast.pl\"}{\"language\"}=\
+-\"C\";\n$PG{\"legacy_blast.pl\"}{\"language2\"}=\"\
+-C\";\n$PG{\"legacy_blast.pl\"}{\"source\"}=\"ftp:/\
+LATEST\";\n$PG{\"legacy_blast\"}{\"language\"}=\
+\"C\";\n$PG{\"legacy_blast\"}{\"language2\"}=\"\
+C\";\n$PG{\"legacy_blast\"}{\"source\"}=\"ftp:/\
+ /ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6\
+ .0/ncbi-blast-2.6.0+-src.tar.gz\";\n$PG{\"legacy_b\
+-last.pl\"}{\"update_action\"}=\"never\";\n$PG{\"le\
+-gacy_blast.pl\"}{\"mode\"}=\"psicoffee,expresso,3d\
+last\"}{\"update_action\"}=\"never\";\n$PG{\"le\
+gacy_blast\"}{\"mode\"}=\"psicoffee,expresso,3d\
+ coffee\";\n$PG{\"SOAP::Lite\"}{\"4_TCOFFEE\"}=\"SO\
+ APLITE\";\n$PG{\"SOAP::Lite\"}{\"type\"}=\"library\
+ \";\n$PG{\"SOAP::Lite\"}{\"ADDRESS\"}=\"http://cpa\
+--- a/tclinkdb.txt
+++ b/tclinkdb.txt
+@@ -340,15 +340,15 @@ PG wublast.pl source		empty
 PG wublast.pl update_action	never
 PG wublast.pl mode		psicoffee,expresso,accurate
 
@@ -232,7 +177,7 @@ Description: Cope with renaming of scripts in ncbi-blast++
 
 PG blastall 4_TCOFFEE		blastall
 PG blastall type		protein_homology_predictor
-@@ -328,14 +328,14 @@
+@@ -359,14 +359,14 @@ PG blastall source		ftp://ftp.ncbi.nlm.n
 PG blastall update_action	never
 PG blastall mode		psicoffee,expresso,3dcoffee
 
@@ -241,7 +186,7 @@ Description: Cope with renaming of scripts in ncbi-blast++
 -PG legacy_blast.pl ADDRESS	 ftp://ftp.ncbi.nih.gov/blast/executables/LATEST
 -PG legacy_blast.pl language	 C
 -PG legacy_blast.pl language2	 C
-PG legacy_blast.pl source	 empty
+-PG legacy_blast.pl source	 ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz
 -PG legacy_blast.pl update_action never
 -PG legacy_blast.pl mode		 psicoffee,expresso,3dcoffee
 +PG legacy_blast 4_TCOFFEE	 NCBIBLAST
@@ -249,15 +194,15 @@ Description: Cope with renaming of scripts in ncbi-blast++
 +PG legacy_blast ADDRESS	 ftp://ftp.ncbi.nih.gov/blast/executables/LATEST
 +PG legacy_blast language	 C
 +PG legacy_blast language2	 C
-+PG legacy_blast source	 empty
+PG legacy_blast source	 ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz
 +PG legacy_blast update_action never
 +PG legacy_blast mode		 psicoffee,expresso,3dcoffee
 
 PG SOAP::Lite 4_TCOFFEE		SOAPLITE
 PG SOAP::Lite type		library
--- T-COFFEE_distribution_Version_11.00.8cbe486.orig/t_coffee_source/data_headers/programmes_define.h
-+++ T-COFFEE_distribution_Version_11.00.8cbe486/t_coffee_source/data_headers/programmes_define.h
-@@ -120,10 +120,10 @@
+--- a/t_coffee_source/data_headers/programmes_define.h
+++ b/t_coffee_source/data_headers/programmes_define.h
+@@ -131,10 +131,10 @@
 //#define EBIWUBLASTc_ADDRESS "http://www.ebi.ac.uk/Tools/webservices/services/wublast"
 
 
@@ -270,9 +215,9 @@ Description: Cope with renaming of scripts in ncbi-blast++
 #define NCBIBLAST_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"
 
 
--- T-COFFEE_distribution_Version_11.00.8cbe486.orig/t_coffee_source/util_lib/util_constraints_list.c
-+++ T-COFFEE_distribution_Version_11.00.8cbe486/t_coffee_source/util_lib/util_constraints_list.c
-@@ -6666,7 +6666,7 @@
+--- a/t_coffee_source/util_lib/util_constraints_list.c
+++ b/t_coffee_source/util_lib/util_constraints_list.c
+@@ -7459,7 +7459,7 @@ char *** produce_method_file ( char *met
 	sprintf (list[n][0], "blastpgp_client");
 	sprintf (list[n][1], "%s", vtmpnam(NULL));
 	n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");

--- a/debian/patches/series
+++ b/debian/patches/series
@@ -6,6 +6,3 @@ set_proper_dir_permissions.patch
 mayhem.patch
 stable-linking-inputs.patch
 clustalw2.patch
-gcc-7.patch
-# debug.patch
-fix_missing_return.patch
--- a/debian/patches/set_proper_dir_permissions.patch
+++ b/debian/patches/set_proper_dir_permissions.patch
@@ -6,7 +6,7 @@ Description: When creating subdirectories in $HOME do not

 --- a/t_coffee_source/util_lib/util.c
 +++ b/t_coffee_source/util_lib/util.c
-@@ -7714,6 +7714,10 @@ int my_mkdir ( char *dir_in)
+@@ -8723,6 +8723,10 @@ int my_mkdir ( char *dir_in)
   int a, buf;
   char *dir;
 
@@ -17,7 +17,7 @@ Description: When creating subdirectories in $HOME do not
 
   dir=(char*)vcalloc ( strlen (dir_in)+strlen (get_home_4_tcoffee())+100, sizeof (char));
   sprintf ( dir, "%s", dir_in);
-@@ -7733,10 +7737,11 @@ int my_mkdir ( char *dir_in)
+@@ -8742,10 +8746,11 @@ int my_mkdir ( char *dir_in)
 
 	  if (access(dir, F_OK)==-1)
 	    {

--- a/example/proteases_large.fasta
+++ b/example/proteases_large.fasta
--- a/install
+++ b/install
@@ -55,7 +55,7 @@ our $FFLAGS="";

 my $install="all";
 my $default_update_action="no_update";
-########################################################
+###########################################################
 my @required_applications=("wget_OR_curl");
 ########### Mode Definitions ##############################
 #
@@ -128,7 +128,8 @@ our ($ROOT_INSTALL, $NO_QUESTION, $default_update_action,$BINARIES_ONLY,$force,
 if ( ($cl=~/-root/)){$ROOT_INSTALL=1;}
 if ( ($cl=~/-no_question/)){$NO_QUESTION=1;}
 if ( ($cl=~/-update/)){$default_update_action="update";}
-if ( ($cl=~/-binaries/)){$BINARIES_ONLY=1;}
+$BINARIES_ONLY=1;
+if ( ($cl=~/-nobinaries/)){$BINARIES_ONLY=0;}
 if ( ($cl=~/-force/)){$force=1;$default_update_action="update"}
 if ( ($cl=~/-exec=\s*(\S+)/)){$INSTALL_DIR=$1;}
 if ( ($cl=~/-plugins=\s*(\S+)/)){$PLUGINS_DIR=$1;}
@@ -631,7 +632,7 @@ sub install_pg
 	$PG{$pg}{old}=$previous;
 	
 	if ($PG{$pg} {language2} eq "Perl"){&install_perl_package ($pg);}
-	elsif ($BINARIES_ONLY && &install_binary_package ($pg)){$PG{$pg}{from_binary}=1;}
+	elsif ($pg ne "t_coffee" && $BINARIES_ONLY && &install_binary_package ($pg)){$PG{$pg}{from_binary}=1;}
 	elsif (&install_source_package ($pg)){;}
 	else 
 	  {
@@ -1039,6 +1040,7 @@ sub install_source_package
    #
    elsif ( $pg eq "proda")
      {
+	`sed -i '' 's/int errno = 0;/int errno; errno = 0;/' Main.cc`;
 	&add_C_libraries("AlignedFragment.h", "vector", "iostream", "cstring","cstdlib");
 	&add_C_libraries("Main.cc", "vector", "climits");	
 	&add_C_libraries("Sequence.cc", "stdlib.h", "cstdio");	
@@ -1091,6 +1093,7 @@ sub install_source_package
    elsif ( $pg eq "retree")
      {
 	chdir "src";
+	&flush_command ("cp Makefile.unx Makefile");
 	&flush_command ("make $arguments all");
 	&flush_command ("make put");
 	system "cp ../exe/* $BIN";
@@ -1168,11 +1171,7 @@ sub install_binary_package
    
    if (!&supported_os($OS)){return 0;}
    if ( $PG{$pg}{binary}){$name=$PG{$pg}{binary};}
-    else 
-      {
-	$name=$pg;
-	if ( $OS eq "windows"){$name.=".exe";}
-      }
+    else {$name=$pg;}
    
    $download="$WEB_BASE/Packages/Binaries/$OS/$name";
    
@@ -1201,23 +1200,9 @@ sub install_binary_package
 	`gunzip  $name`;
 	`tar -xvf $pg.tar`;
 	chdir $pg;
-	if ( $pg eq "mafft")
-	  {
-	    if ($ROOT_INSTALL)
-	      {
-		&root_run ("You Must be Roor to Install MAFFT\n", "$CP mafft/bin/* /usr/local/mafft;mkdir /usr/local/mafft/; $CP mafft/lib/* /usr/local/bin/");
-	      }
-	    else
-	      {
-		`$CP $TMP/$pg/bin/* $BIN $SILENT`;
-		`$CP $TMP/$pg/lib/* $BIN $SILENT`;
-	      }
-	  }
-	else
-	  {
-	    if (-e "$TMP/$pg/data"){`$CP $TMP/$pg/data/* $TCM $SILENT`;}
-	    if (!($pg=~/\*/)){`rm -rf $pg`;}
-	  }
+	`chmod u+x *`;
+ 	`mv * $BIN`;
+	#if (!($pg=~/\*/)){`rm -rf $pg`;}
      }
    else
      {
@@ -1331,6 +1316,8 @@ sub repo_load
 {
    my ($pg)=(@_);

+    #Bypass the Repository Cache
+    return 0;
    # check that all required data are available
    if( $REPO_ROOT eq "" ) { return 0; }

@@ -1558,7 +1545,7 @@ $PG{"t_coffee"}{"type"}="sequence_multiple_aligner";
 $PG{"t_coffee"}{"ADDRESS"}="http://www.tcoffee.org";
 $PG{"t_coffee"}{"language"}="C++";
 $PG{"t_coffee"}{"language2"}="CXX";
-$PG{"t_coffee"}{"source"}="http://www.tcoffee.org/Packages/T-COFFEE_distribution.tar.gz";
+$PG{"t_coffee"}{"source"}="http://www.tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution.tar.gz";
 $PG{"t_coffee"}{"update_action"}="always";
 $PG{"t_coffee"}{"mode"}="tcoffee,mcoffee,rcoffee,expresso,3dcoffee";
 $PG{"clustalo"}{"4_TCOFFEE"}="CLUSTALO";
@@ -1566,9 +1553,10 @@ $PG{"clustalo"}{"type"}="sequence_multiple_aligner";
 $PG{"clustalo"}{"ADDRESS"}="http://www.clustal.org/omega/";
 $PG{"clustalo"}{"language"}="C++";
 $PG{"clustalo"}{"language2"}="C++";
-$PG{"clustalo"}{"source"}="http://www.clustal.org/omega/clustal-omega-1.1.0.tar.gz";
+$PG{"clustalo"}{"source"}="http://www.clustal.org/omega/clustal-omega-1.2.4.tar.gz";
 $PG{"clustalo"}{"mode"}="mcoffee";
-$PG{"clustalo"}{"version"}="1.1.0";
+$PG{"clustalo"}{"binary"}="clustalo";
+$PG{"clustalo"}{"version"}="1.2.4";
 $PG{"strike"}{"4_TCOFFEE"}="STRIKE";
 $PG{"strike"}{"type"}="sequence_alignment_scoring";
 $PG{"strike"}{"ADDRESS"}="http://www.tcoffee.org/Projects/strike/index.html";
@@ -1633,16 +1621,55 @@ $PG{"probcons"}{"source"}="http://probcons.stanford.edu/probcons_v1_12.tar.gz";
 $PG{"probcons"}{"mode"}="mcoffee";
 $PG{"probcons"}{"binary"}="probcons";
 $PG{"probcons"}{"version"}="1.12";
+$PG{"msaprobs"}{"4_TCOFFEE"}="MSAPROBS";
+$PG{"msaprobs"}{"type"}="sequence_multiple_aligner";
+$PG{"msaprobs"}{"ADDRESS"}="http://msaprobs.sourceforge.net/homepage.htm#latest";
+$PG{"msaprobs"}{"language2"}="CXX";
+$PG{"msaprobs"}{"language"}="C++";
+$PG{"msaprobs"}{"source"}="https://sourceforge.net/projects/msaprobs/files/MSAProbs-MPI/MSAProbs-MPI_rel1.0.5.tar.gz";
+$PG{"msaprobs"}{"mode"}="mcoffee";
+$PG{"msaprobs"}{"binary"}="msaprobs";
+$PG{"msaprobs"}{"version"}="1.05";
+$PG{"msaprobs"}{"update_action"}="never";
+$PG{"upp"}{"4_TCOFFEE"}="UPP";
+$PG{"upp"}{"type"}="sequence_multiple_aligner";
+$PG{"upp"}{"ADDRESS"}="http://www.cs.utexas.edu/users/phylo/software/upp/";
+$PG{"upp"}{"language2"}="CXX";
+$PG{"upp"}{"language"}="C++";
+$PG{"upp"}{"source"}="https://github.com/smirarab/pasta/archive/upp.zip";
+$PG{"upp"}{"mode"}="mcoffee";
+$PG{"upp"}{"binary"}="upp";
+$PG{"upp"}{"version"}="1";
+$PG{"upp"}{"update_action"}="never";
 $PG{"mafft"}{"4_TCOFFEE"}="MAFFT";
 $PG{"mafft"}{"type"}="sequence_multiple_aligner";
 $PG{"mafft"}{"ADDRESS"}="http://align.bmr.kyushu-u.ac.jp/mafft/online/server/";
 $PG{"mafft"}{"language"}="C";
 $PG{"mafft"}{"language"}="C";
-$PG{"mafft"}{"source"}="http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-with-extensions-src.tgz";
-$PG{"mafft"}{"windows"}="http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-mingw.tar";
+$PG{"mafft"}{"source"}="http://mafft.cbrc.jp/alignment/software/mafft-7.310-with-extensions-src.tgz";
 $PG{"mafft"}{"mode"}="mcoffee,rcoffee";
 $PG{"mafft"}{"binary"}="mafft.tar.gz";
-$PG{"mafft"}{"version"}="6.603";
+$PG{"mafft"}{"version"}="7.310";
+$PG{"msa"}{"4_TCOFFEE"}="MSA";
+$PG{"msa"}{"type"}="sequence_multiple_aligner";
+$PG{"msa"}{"ADDRESS"}="https://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/msa.html";
+$PG{"msa"}{"language"}="C";
+$PG{"msa"}{"language"}="C";
+$PG{"msa"}{"source"}="ftp://ftp.ncbi.nih.gov/pub/msa/msa.tar.Z";
+$PG{"msa"}{"mode"}="mcoffee";
+$PG{"msa"}{"binary"}="msa.pl";
+$PG{"msa"}{"version"}="1.0";
+$PG{"msa"}{"update_action"}="never";
+$PG{"dca"}{"4_TCOFFEE"}="DCA";
+$PG{"dca"}{"type"}="sequence_multiple_aligner";
+$PG{"dca"}{"ADDRESS"}="https://bibiserv2.cebitec.uni-bielefeld.de/dca";
+$PG{"dca"}{"language"}="C";
+$PG{"dca"}{"language"}="C";
+$PG{"dca"}{"source"}="https://bibiserv2.cebitec.uni-bielefeld.de/applications/dca/resources/downloads/dca-1.1-src.tar.gz";
+$PG{"dca"}{"mode"}="mcoffee";
+$PG{"dca"}{"binary"}="dca.pl";
+$PG{"dca"}{"version"}="1.1";
+$PG{"dca"}{"update_action"}="never";
 $PG{"muscle"}{"4_TCOFFEE"}="MUSCLE";
 $PG{"muscle"}{"type"}="sequence_multiple_aligner";
 $PG{"muscle"}{"ADDRESS"}="http://www.drive5.com/muscle/";
@@ -1653,20 +1680,12 @@ $PG{"muscle"}{"windows"}="http://www.drive5.com/muscle/downloads3.7/muscle3.7_wi
 $PG{"muscle"}{"linux"}="http://www.drive5.com/muscle/downloads3.7/muscle3.7_linux_ia32.tar.gz";
 $PG{"muscle"}{"mode"}="mcoffee,rcoffee";
 $PG{"muscle"}{"version"}="3.7";
-$PG{"mus4"}{"4_TCOFFEE"}="MUS4";
-$PG{"mus4"}{"type"}="sequence_multiple_aligner";
-$PG{"mus4"}{"ADDRESS"}="http://www.drive5.com/muscle/";
-$PG{"mus4"}{"language"}="C++";
-$PG{"mus4"}{"language2"}="GPP";
-$PG{"mus4"}{"source"}="http://www.drive5.com/muscle/muscle4.0_src.tar.gz";
-$PG{"mus4"}{"mode"}="mcoffee,rcoffee";
-$PG{"mus4"}{"version"}="4.0";
 $PG{"pcma"}{"4_TCOFFEE"}="PCMA";
 $PG{"pcma"}{"type"}="sequence_multiple_aligner";
-$PG{"pcma"}{"ADDRESS"}="ftp://iole.swmed.edu/pub/PCMA/";
+$PG{"pcma"}{"ADDRESS"}="http://prodata.swmed.edu/pcma/pcma.php";
 $PG{"pcma"}{"language"}="C";
 $PG{"pcma"}{"language2"}="C";
-$PG{"pcma"}{"source"}="ftp://iole.swmed.edu/pub/PCMA/pcma.tar.gz";
+$PG{"pcma"}{"source"}="http://prodata.swmed.edu/download/pub/PCMA/pcma.tar.gz";
 $PG{"pcma"}{"mode"}="mcoffee";
 $PG{"pcma"}{"version"}="1.0";
 $PG{"kalign"}{"4_TCOFFEE"}="KALIGN";
@@ -1682,9 +1701,10 @@ $PG{"amap"}{"type"}="sequence_multiple_aligner";
 $PG{"amap"}{"ADDRESS"}="http://bio.math.berkeley.edu/amap/";
 $PG{"amap"}{"language"}="C++";
 $PG{"amap"}{"language2"}="CXX";
-$PG{"amap"}{"source"}="http://amap-align.googlecode.com/files/amap.2.0.tar.gz";
+$PG{"amap"}{"source"}="https://github.com/mes5k/amap-align/archive/amap.zip";
 $PG{"amap"}{"mode"}="mcoffee";
 $PG{"amap"}{"version"}="2.0";
+$PG{"amap"}{"update_action"}="never";
 $PG{"proda"}{"4_TCOFFEE"}="PRODA";
 $PG{"proda"}{"type"}="sequence_multiple_aligner";
 $PG{"proda"}{"ADDRESS"}="http://proda.stanford.edu";
@@ -1693,14 +1713,6 @@ $PG{"proda"}{"language2"}="CXX";
 $PG{"proda"}{"source"}="http://proda.stanford.edu/proda_1_0.tar.gz";
 $PG{"proda"}{"mode"}="mcoffee";
 $PG{"proda"}{"version"}="1.0";
-$PG{"fsa"}{"4_TCOFFEE"}="FSA";
-$PG{"fsa"}{"type"}="sequence_multiple_aligner";
-$PG{"fsa"}{"ADDRESS"}="http://fsa.sourceforge.net/";
-$PG{"fsa"}{"language"}="C++";
-$PG{"fsa"}{"language2"}="CXX";
-$PG{"fsa"}{"source"}="http://sourceforge.net/projects/fsa/files/fsa-1.15.3.tar.gz/download/";
-$PG{"fsa"}{"mode"}="mcoffee";
-$PG{"fsa"}{"version"}="1.15.3";
 $PG{"prank"}{"4_TCOFFEE"}="PRANK";
 $PG{"prank"}{"type"}="sequence_multiple_aligner";
 $PG{"prank"}{"ADDRESS"}="http://www.ebi.ac.uk/goldman-srv/prank/";
@@ -1711,10 +1723,10 @@ $PG{"prank"}{"mode"}="mcoffee";
 $PG{"prank"}{"version"}="100303";
 $PG{"sap"}{"4_TCOFFEE"}="SAP";
 $PG{"sap"}{"type"}="structure_pairwise_aligner";
-$PG{"sap"}{"ADDRESS"}="http://mathbio.nimr.mrc.ac.uk/wiki/Software";
+$PG{"sap"}{"ADDRESS"}="https://mathbio.crick.ac.uk/wiki/Software#SAP";
 $PG{"sap"}{"language"}="C";
 $PG{"sap"}{"language2"}="C";
-$PG{"sap"}{"source"}="http://mathbio.nimr.mrc.ac.uk/download/SAP/sap-1.1.3.tar.gz";
+$PG{"sap"}{"source"}="https://github.com/jkleinj/SAP/archive/v.1.1.3.tar.gz";
 $PG{"sap"}{"mode"}="expresso,3dcoffee";
 $PG{"sap"}{"version"}="1.1.3";
 $PG{"TMalign"}{"4_TCOFFEE"}="TMALIGN";
@@ -1728,12 +1740,12 @@ $PG{"TMalign"}{"mode"}="expresso,3dcoffee";
 $PG{"TMalign"}{"version"}="2013.05.11";
 $PG{"mustang"}{"4_TCOFFEE"}="MUSTANG";
 $PG{"mustang"}{"type"}="structure_pairwise_aligner";
-$PG{"mustang"}{"ADDRESS"}="http://www.cs.mu.oz.au/~arun/mustang";
+$PG{"mustang"}{"ADDRESS"}="http://lcb.infotech.monash.edu.au/mustang/";
 $PG{"mustang"}{"language"}="C++";
 $PG{"mustang"}{"language2"}="CXX";
-$PG{"mustang"}{"source"}="http://ww2.cs.mu.oz.au/~arun/mustang/mustang_v3.2.1.tgz";
+$PG{"mustang"}{"source"}="http://lcb.infotech.monash.edu.au/mustang/mustang_v3.2.3.tgz";
 $PG{"mustang"}{"mode"}="expresso,3dcoffee";
-$PG{"mustang"}{"version"}="3.2.1";
+$PG{"mustang"}{"version"}="3.2.3";
 $PG{"lsqman"}{"4_TCOFFEE"}="LSQMAN";
 $PG{"lsqman"}{"type"}="structure_pairwise_aligner";
 $PG{"lsqman"}{"ADDRESS"}="empty";
@@ -1752,7 +1764,7 @@ $PG{"align_pdb"}{"update_action"}="never";
 $PG{"align_pdb"}{"mode"}="expresso,3dcoffee";
 $PG{"fugueali"}{"4_TCOFFEE"}="FUGUE";
 $PG{"fugueali"}{"type"}="structure_pairwise_aligner";
-$PG{"fugueali"}{"ADDRESS"}="http://www-cryst.bioc.cam.ac.uk/fugue/download.html";
+$PG{"fugueali"}{"ADDRESS"}="http://mizuguchilab.org/fugue/";
 $PG{"fugueali"}{"language"}="empty";
 $PG{"fugueali"}{"language2"}="empty";
 $PG{"fugueali"}{"source"}="empty";
@@ -1785,26 +1797,28 @@ $PG{"sfold"}{"update_action"}="never";
 $PG{"sfold"}{"mode"}="rcoffee";
 $PG{"RNAplfold"}{"4_TCOFFEE"}="RNAPLFOLD";
 $PG{"RNAplfold"}{"type"}="RNA_secondarystructure_predictor";
-$PG{"RNAplfold"}{"ADDRESS"}="http://www.tbi.univie.ac.at/~ivo/RNA/";
+$PG{"RNAplfold"}{"ADDRESS"}="http://www.tbi.univie.ac.at/RNA/";
 $PG{"RNAplfold"}{"language"}="C";
 $PG{"RNAplfold"}{"language2"}="C";
-$PG{"RNAplfold"}{"source"}="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.7.2.tar.gz";
+$PG{"RNAplfold"}{"source"}="http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.9.tar.gz";
 $PG{"RNAplfold"}{"mode"}="rcoffee,";
-$PG{"RNAplfold"}{"version"}="1.7.2";
+$PG{"RNAplfold"}{"binary"}="RNAplfold.tar.gz";
+$PG{"RNAplfold"}{"version"}="2.1.9";
 $PG{"retree"}{"4_TCOFFEE"}="PHYLIP";
-$PG{"retree"}{"type"}="RNA_secondarystructure_predictor";
+$PG{"retree"}{"type"}="Phylogeny";
 $PG{"retree"}{"ADDRESS"}="http://evolution.gs.washington.edu/phylip/";
 $PG{"retree"}{"language"}="C";
 $PG{"retree"}{"language2"}="C";
-$PG{"retree"}{"source"}="http://evolution.gs.washington.edu/phylip/download/phylip-3.69.tar.gz";
+$PG{"retree"}{"source"}="http://www.tcoffee.org/Packages/mirrors/source/phylip-3.66.tar.gz";
 $PG{"retree"}{"mode"}="trmsd,";
-$PG{"retree"}{"version"}="3.69";
+$PG{"retree"}{"binary"}="retree.tar.gz";
+$PG{"retree"}{"version"}="3.66";
 $PG{"hmmtop"}{"4_TCOFFEE"}="HMMTOP";
 $PG{"hmmtop"}{"type"}="protein_secondarystructure_predictor";
 $PG{"hmmtop"}{"ADDRESS"}="www.enzim.hu/hmmtop/";
 $PG{"hmmtop"}{"language"}="C";
 $PG{"hmmtop"}{"language2"}="C";
-$PG{"hmmtop"}{"source"}="empty";
+$PG{"hmmtop"}{"source"}="http://www.tcoffee.org/Packages/mirrors/hmmtop2.1.tgz";
 $PG{"hmmtop"}{"binary"}="hmmtop";
 $PG{"hmmtop"}{"update_action"}="never";
 $PG{"hmmtop"}{"mode"}="tcoffee";
@@ -1814,7 +1828,7 @@ $PG{"gorIV"}{"type"}="protein_secondarystructure_predictor";
 $PG{"gorIV"}{"ADDRESS"}="http://mig.jouy.inra.fr/logiciels/gorIV/";
 $PG{"gorIV"}{"language"}="C";
 $PG{"gorIV"}{"language2"}="C";
-$PG{"gorIV"}{"source"}="http://mig.jouy.inra.fr/logiciels/gorIV/GOR_IV.tar.gz";
+$PG{"gorIV"}{"source"}="http://www.tcoffee.org/Packages/mirrors/GOR_IV.tar.gz";
 $PG{"gorIV"}{"update_action"}="never";
 $PG{"gorIV"}{"mode"}="tcoffee";
 $PG{"wublast.pl"}{"4_TCOFFEE"}="EBIWUBLASTc";
@@ -1840,7 +1854,7 @@ $PG{"blastall"}{"type"}="protein_homology_predictor";
 $PG{"blastall"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
 $PG{"blastall"}{"language"}="C";
 $PG{"blastall"}{"language2"}="C";
-$PG{"blastall"}{"source"}="empty";
+$PG{"blastall"}{"source"}="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz";
 $PG{"blastall"}{"update_action"}="never";
 $PG{"blastall"}{"mode"}="psicoffee,expresso,3dcoffee";
 $PG{"legacy_blast.pl"}{"4_TCOFFEE"}="NCBIBLAST";
@@ -1848,7 +1862,7 @@ $PG{"legacy_blast.pl"}{"type"}="protein_homology_predictor";
 $PG{"legacy_blast.pl"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
 $PG{"legacy_blast.pl"}{"language"}="C";
 $PG{"legacy_blast.pl"}{"language2"}="C";
-$PG{"legacy_blast.pl"}{"source"}="empty";
+$PG{"legacy_blast.pl"}{"source"}="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz";
 $PG{"legacy_blast.pl"}{"update_action"}="never";
 $PG{"legacy_blast.pl"}{"mode"}="psicoffee,expresso,3dcoffee";
 $PG{"SOAP::Lite"}{"4_TCOFFEE"}="SOAPLITE";
@@ -1857,7 +1871,7 @@ $PG{"SOAP::Lite"}{"ADDRESS"}="http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite-0
 $PG{"SOAP::Lite"}{"language"}="Perl";
 $PG{"SOAP::Lite"}{"language2"}="Perl";
 $PG{"SOAP::Lite"}{"source"}="empty";
-$PG{"blastpgp"}{"update_action"}="never";
+$PG{"SOAP::Lite"}{"update_action"}="never";
 $PG{"SOAP::Lite"}{"mode"}="none";
 $PG{"XML::Simple"}{"4_TCOFFEE"}="XMLSIMPLE";
 $PG{"XML::Simple"}{"type"}="library";
@@ -1866,6 +1880,30 @@ $PG{"XML::Simple"}{"language"}="Perl";
 $PG{"XML::Simple"}{"language2"}="Perl";
 $PG{"XML::Simple"}{"source"}="empty";
 $PG{"XML::Simple"}{"mode"}="psicoffee,expresso,accurate";
+$PG{"x3dna"}{"4_TCOFFEE"}="x3dna-ssr";
+$PG{"x3dna"}{"type"}="RNA_secondarystructure_predictor";
+$PG{"x3dna"}{"ADDRESS"}="http://x3dna.bio.columbia.edu/";
+$PG{"x3dna"}{"source"}="http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz";
+$PG{"x3dna"}{"mode"}="saracoffee";
+$PG{"x3dna"}{"update_action"}="never";
+$PG{"fsa"}{"4_TCOFFEE"}="FSA";
+$PG{"fsa"}{"type"}="sequence_multiple_aligner";
+$PG{"fsa"}{"ADDRESS"}="http://fsa.sourceforge.net/";
+$PG{"fsa"}{"language"}="C++";
+$PG{"fsa"}{"language2"}="CXX";
+$PG{"fsa"}{"source"}="http://sourceforge.net/projects/fsa/files/fsa-1.15.3.tar.gz/download/";
+$PG{"fsa"}{"mode"}="mcoffee";
+$PG{"fsa"}{"version"}="1.15.3";
+$PG{"fsa"}{"update_action"}="never";
+$PG{"mus4"}{"4_TCOFFEE"}="MUS4";
+$PG{"mus4"}{"type"}="sequence_multiple_aligner";
+$PG{"mus4"}{"ADDRESS"}="http://www.drive5.com/muscle/";
+$PG{"mus4"}{"language"}="C++";
+$PG{"mus4"}{"language2"}="GPP";
+$PG{"mus4"}{"source"}="http://www.drive5.com/muscle/muscle4.0_src.tar.gz";
+$PG{"mus4"}{"mode"}="mcoffee,rcoffee";
+$PG{"mus4"}{"version"}="4.0";
+$PG{"mus4"}{"update_action"}="never";
 $MODE{"tcoffee"}{"name"}="tcoffee";
 $MODE{"rcoffee"}{"name"}="rcoffee";
 $MODE{"3dcoffee"}{"name"}="3dcoffee";

--- a/license.txt
+++ b/license.txt
 -------------------------------COPYRIGHT NOTICE------------------------------/
  ACADEMIC LICENCE AGREEMENT

-  © Centro de Regulacio Genomica and Cedric Notredame  ( 12 Aug 2014 - 22:07). 
+  © Centro de Regulacio Genomica and Cedric Notredame  ( 11 Dec 2018 - 09:27). 
 		    GNU GENERAL PUBLIC LICENSE
 		       Version 2, June 1991


--- a/t_coffee_source/coffee_defines.h
+++ b/t_coffee_source/coffee_defines.h
@@ -2,7 +2,7 @@
 /*  (c) Centro de Regulacio Genomica                                                        */
 /*  and                                                                                     */
 /*  Cedric Notredame                                                                        */
-/*  12 Aug 2014 - 22:07.                                                                    */
+/*  11 Dec 2018 - 09:27.                                                                    */
 /*All rights reserved.                                                                      */
 /*This file is part of T-COFFEE.                                                            */
 /*                                                                                          */
@@ -21,7 +21,7 @@
 /*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
 /*...............................................                                           */
 /*  If you need some more information                                                       */
-/*  cedric.notredame@europe.com                                                             */
+/*  cedric.notredame@gmail.com                                                             */
 /*...............................................                                           */
 /******************************COPYRIGHT NOTICE*******************************/
 #ifndef COFFEE_DEFINES_H
@@ -59,6 +59,11 @@
 #define GIVE_MEMORY_BACK 0
 #define MEMSET0   1
 #define NO_MEMSET0 0
+#define MEMSET 1
+#define NOMEMSET -1
+#define RESIZE 1
+#define NORESIZE -1
+
 /*OUTPUT DEFINITIONS*/
 #define  NO_COLOR_RESIDUE 127
 #define  NO_COLOR_GAP 126
@@ -82,7 +87,7 @@
 #define NOTEMPLATES 0

 #define EXTEND 1
-#define RESIZE 2
+

 #define SEN                0 
 #define SPE                1 
@@ -275,7 +280,7 @@
 #define MAX_N_LIST       100

 #define COMMENT_SIZE     1000
-#define MAXNAMES         100
+#define MAXNAMES         1000
 #define FILENAMELEN 	 500            /* Max. file name length */
 #define MAX_N_PARAM      2000
 #define MAX_PARAM_LEN    200
@@ -411,4 +416,7 @@
 #define NULL_6 NULL_4,NULL_2
 #define NULL_7 NULL_5,NULL_2

+
+#define PATCH_PRF ""
+//This variable is set so as to compensate a bug in Clustal-Omega
 #endif // -- COFFEE_DEFINES_H
--- a/t_coffee_source/data_headers/perl_header_lib.h
+++ b/t_coffee_source/data_headers/perl_header_lib.h
@@ -2,7 +2,7 @@
 /*  (c) Centro de Regulacio Genomica                                                        */
 /*  and                                                                                     */
 /*  Cedric Notredame                                                                        */
-/*  12 Aug 2014 - 22:07.                                                                    */
+/*  11 Dec 2018 - 09:27.                                                                    */
 /*All rights reserved.                                                                      */
 /*This file is part of T-COFFEE.                                                            */
 /*                                                                                          */
@@ -21,7 +21,7 @@
 /*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
 /*...............................................                                           */
 /*  If you need some more information                                                       */
-/*  cedric.notredame@europe.com                                                             */
+/*  cedric.notredame@gmail.com                                                             */
 /*...............................................                                           */
 /******************************COPYRIGHT NOTICE*******************************/
 /*

--- a/t_coffee_source/data_headers/programmes_define.h
+++ b/t_coffee_source/data_headers/programmes_define.h
@@ -2,7 +2,7 @@
 /*  (c) Centro de Regulacio Genomica                                                        */
 /*  and                                                                                     */
 /*  Cedric Notredame                                                                        */
-/*  12 Aug 2014 - 22:07.                                                                    */
+/*  11 Dec 2018 - 09:27.                                                                    */
 /*All rights reserved.                                                                      */
 /*This file is part of T-COFFEE.                                                            */
 /*                                                                                          */
@@ -21,7 +21,7 @@
 /*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
 /*...............................................                                           */
 /*  If you need some more information                                                       */
-/*  cedric.notredame@europe.com                                                             */
+/*  cedric.notredame@gmail.com                                                             */
 /*...............................................                                           */
 /******************************COPYRIGHT NOTICE*******************************/
 /* PROGRAM PATH - DO NOT CHANGE MANUALLY THIS FILE -- It is generated automatically by the build process -- See the 'update' target in the 'makefile' for more details */
@@ -72,6 +72,11 @@
 #define PROBCONS_ADDRESS  "http://probcons.stanford.edu/"


+#define MSAPROBS_4_TCOFFEE "probcons"
+#define MSAPROBS_4_TCOFFEE "probconsRNA"
+#define MSAPROBS_ADDRESS   "http://msaprobs.sourceforge.net/homepage.htm#latest"
+
+


 #define DIALIGNT_4_TCOFFEE "dialign-t"
@@ -82,6 +87,12 @@
 #define DIALIGNTX_ADDRESS  "http://dialign-tx.gobics.de/"
 #define DIALIGNTX_DIR "/usr/share/dialign-tx/"

+#define MSA_4_TCOFFEE "msa.pl"
+#define MSA_ADDRESS "https://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/msa.html"
+
+#define DCA_4_TCOFFEE "dca.pl"
+#define DCA_ADDRESS "https://bibiserv2.cebitec.uni-bielefeld.de/applications/dca/resources/downloads/dca-1.1-src.tar.gz"
+
 #define MAFFT_4_TCOFFEE "mafft"
 #define MAFFT_ADDRESS "http://align.bmr.kyushu-u.ac.jp/mafft/online/server/"


--- a/t_coffee_source/define_header.h
+++ b/t_coffee_source/define_header.h
@@ -2,7 +2,7 @@
 /*  (c) Centro de Regulacio Genomica                                                        */
 /*  and                                                                                     */
 /*  Cedric Notredame                                                                        */
-/*  12 Aug 2014 - 22:07.                                                                    */
+/*  11 Dec 2018 - 09:27.                                                                    */
 /*All rights reserved.                                                                      */
 /*This file is part of T-COFFEE.                                                            */
 /*                                                                                          */
@@ -21,7 +21,7 @@
 /*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
 /*...............................................                                           */
 /*  If you need some more information                                                       */
-/*  cedric.notredame@europe.com                                                             */
+/*  cedric.notredame@gmail.com                                                             */
 /*...............................................                                           */
 /******************************COPYRIGHT NOTICE*******************************/
 #ifndef DEFINE_HEADER_H
@@ -34,9 +34,9 @@
 // the following constants are updated during the build process -- see the 'makefile' for details
 #define PROGRAM "T-COFFEE"
 #define AUTHOR "Cedric Notredame "
-#define DATE "12 Aug 2014 - 22:05"
-#define VERSION "Version_11.00.8cbe486"
-#define BUILD_INFO "2014-08-12 22:05:29 - Revision 8cbe486 - Build 477"
+#define DATE "11 Dec 2018 - 09:27"
+#define VERSION "Version_12.00.7fb08c2"
+#define BUILD_INFO "2018-12-11 09:27:12 - Revision 7fb08c2 - Build 211"
 #define DISTRIBUTION_ADDRESS "www.tcoffee.org/Packages"



--- a/t_coffee_source/dev1_lib_header.h
+++ b/t_coffee_source/dev1_lib_header.h
@@ -2,7 +2,7 @@
 /*  (c) Centro de Regulacio Genomica                                                        */
 /*  and                                                                                     */
 /*  Cedric Notredame                                                                        */
-/*  12 Aug 2014 - 22:07.                                                                    */
+/*  11 Dec 2018 - 09:27.                                                                    */
 /*All rights reserved.                                                                      */
 /*This file is part of T-COFFEE.                                                            */
 /*                                                                                          */
@@ -21,7 +21,7 @@
 /*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
 /*...............................................                                           */
 /*  If you need some more information                                                       */
-/*  cedric.notredame@europe.com                                                             */
+/*  cedric.notredame@gmail.com                                                             */
 /*...............................................                                           */
 /******************************COPYRIGHT NOTICE*******************************/
 #ifndef DEV1_LIB_HEADER_H

--- a/t_coffee_source/dev_lib/dev1.c
+++ b/t_coffee_source/dev_lib/dev1.c
@@ -2,7 +2,7 @@
 /*  (c) Centro de Regulacio Genomica                                                        */
 /*  and                                                                                     */
 /*  Cedric Notredame                                                                        */
-/*  12 Aug 2014 - 22:07.                                                                    */
+/*  11 Dec 2018 - 09:27.                                                                    */
 /*All rights reserved.                                                                      */
 /*This file is part of T-COFFEE.                                                            */
 /*                                                                                          */
@@ -21,7 +21,7 @@
 /*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
 /*...............................................                                           */
 /*  If you need some more information                                                       */
-/*  cedric.notredame@europe.com                                                             */
+/*  cedric.notredame@gmail.com                                                             */
 /*...............................................                                           */
 /******************************COPYRIGHT NOTICE*******************************/
 #include <stdio.h>

--- a/t_coffee_source/dev_lib/dev1.h
+++ b/t_coffee_source/dev_lib/dev1.h
@@ -2,7 +2,7 @@
 /*  (c) Centro de Regulacio Genomica                                                        */
 /*  and                                                                                     */
 /*  Cedric Notredame                                                                        */
-/*  12 Aug 2014 - 22:07.                                                                    */
+/*  11 Dec 2018 - 09:27.                                                                    */
 /*All rights reserved.                                                                      */
 /*This file is part of T-COFFEE.                                                            */
 /*                                                                                          */
@@ -21,7 +21,7 @@
 /*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
 /*...............................................                                           */
 /*  If you need some more information                                                       */
-/*  cedric.notredame@europe.com                                                             */
+/*  cedric.notredame@gmail.com                                                             */
 /*...............................................                                           */
 /******************************COPYRIGHT NOTICE*******************************/
 #ifndef DEV1_H

--- a/t_coffee_source/dp_lib/CUSTOM_evaluate_for_struc.c
+++ b/t_coffee_source/dp_lib/CUSTOM_evaluate_for_struc.c
@@ -2,7 +2,7 @@
 /*  (c) Centro de Regulacio Genomica                                                        */
 /*  and                                                                                     */
 /*  Cedric Notredame                                                                        */
-/*  12 Aug 2014 - 22:07.                                                                    */
+/*  11 Dec 2018 - 09:27.                                                                    */
 /*All rights reserved.                                                                      */
 /*This file is part of T-COFFEE.                                                            */
 /*                                                                                          */
@@ -21,7 +21,7 @@
 /*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
 /*...............................................                                           */
 /*  If you need some more information                                                       */
-/*  cedric.notredame@europe.com                                                             */
+/*  cedric.notredame@gmail.com                                                             */
 /*...............................................                                           */
 /******************************COPYRIGHT NOTICE*******************************/
 #include <stdio.h>