Date: Wed, 31 Oct 2007 10:39:56 GMT From: Motomichi Matsuzaki <mzaki@e-mail.ne.jp> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/117713: Update port: biology/clustalw to 2.0 Message-ID: <200710311039.l9VAduRm080120@www.freebsd.org> Resent-Message-ID: <200710311040.l9VAe1Kj028206@freefall.freebsd.org>
next in thread | raw e-mail | index | archive | help
>Number: 117713 >Category: ports >Synopsis: Update port: biology/clustalw to 2.0 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Wed Oct 31 10:40:00 UTC 2007 >Closed-Date: >Last-Modified: >Originator: Motomichi Matsuzaki >Release: >Organization: >Environment: >Description: This version has been completely rewritten in C++. Also minor improvements were introduced: * New option for calculating guide trees with UPGMA method allowing faster alignment on large datasets, however less accurate. * "Remove first" iteration method for refining alignments. >How-To-Repeat: >Fix: Patch attached with submission follows: diff -ruN clustalw.orig/Makefile clustalw/Makefile --- clustalw.orig/Makefile Sun Mar 11 12:20:27 2007 +++ clustalw/Makefile Wed Oct 31 17:58:32 2007 @@ -6,21 +6,21 @@ # PORTNAME= clustalw -PORTVERSION= 1.83 +PORTVERSION= 2.0 CATEGORIES= biology -MASTER_SITES= ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/ -DISTNAME= ${PORTNAME}${PORTVERSION}.UNIX +MASTER_SITES= ftp://ftp.ebi.ac.uk/pub/software/clustalw2/ +DISTNAME= ${PORTNAME}-linux-src-${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= CLUSTAL W Multiple Sequence Alignment Program WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION} -MAKEFILE= makefile ALL_TARGET= # empty do-install: - ${INSTALL_PROGRAM} ${WRKSRC}/clustalw ${PREFIX}/bin + ${INSTALL_PROGRAM} ${WRKSRC}/clustalw2 ${PREFIX}/bin + ${LN} -sf clustalw2 ${PREFIX}/bin/clustalw @${MKDIR} ${DATADIR} ${INSTALL_DATA} ${WRKSRC}/clustalw_help ${DATADIR} diff -ruN clustalw.orig/distinfo clustalw/distinfo --- clustalw.orig/distinfo Sun Jan 22 17:20:29 2006 +++ clustalw/distinfo Wed Oct 31 16:09:57 2007 @@ -1,3 +1,3 @@ -MD5 (clustalw1.83.UNIX.tar.gz) = dc240277e5bb14ffc106d4a5fda87752 -SHA256 (clustalw1.83.UNIX.tar.gz) = 8b757e02ae95ac0a0dd37db640497aa90f7a13a11784ce2a17f41b64e3059c60 -SIZE (clustalw1.83.UNIX.tar.gz) = 166863 +MD5 (clustalw-linux-src-2.0.tar.gz) = 04bb7bad022dad39bafc1db8c6d64446 +SHA256 (clustalw-linux-src-2.0.tar.gz) = e10c456f45f892936903069638271df6fb4bf30a84d0362ce62031f058408ded +SIZE (clustalw-linux-src-2.0.tar.gz) = 274726 diff -ruN clustalw.orig/files/patch-Makefile clustalw/files/patch-Makefile --- clustalw.orig/files/patch-Makefile Thu Jan 1 09:00:00 1970 +++ clustalw/files/patch-Makefile Wed Oct 31 17:42:46 2007 @@ -0,0 +1,13 @@ +--- Makefile.orig Wed Aug 8 18:21:23 2007 ++++ Makefile Wed Oct 31 17:35:20 2007 +@@ -51,8 +51,8 @@ + compiledObjects/RootedClusterTree.o compiledObjects/Iteration.o \ + compiledObjects/InFileStream.o compiledObjects/ClustalWResources.o + +-CXX = g++ +-CXXFLAGS = -c -O2 ++CXX ?= g++ ++CXXFLAGS += -c -DDATADIR=\"${PREFIX}/share/clustalw\" + LFLAGS = -g + + clustalw2: $(OBJECTS) diff -ruN clustalw.orig/files/patch-aa clustalw/files/patch-aa --- clustalw.orig/files/patch-aa Sun Feb 16 03:43:14 2003 +++ clustalw/files/patch-aa Thu Jan 1 09:00:00 1970 @@ -1,11 +0,0 @@ ---- clustalw.c.orig Thu Feb 13 15:17:15 2003 -+++ clustalw.c Thu Feb 13 14:50:51 2003 -@@ -34,7 +34,7 @@ - #ifdef MSDOS - char *help_file_name = "clustalw.hlp"; - #else -- char *help_file_name = "clustalw_help"; -+ char *help_file_name = DATADIR "/clustalw_help"; - #endif - - sint max_names; /* maximum length of names in current alignment file */ diff -ruN clustalw.orig/files/patch-ab clustalw/files/patch-ab --- clustalw.orig/files/patch-ab Sun Feb 16 03:43:14 2003 +++ clustalw/files/patch-ab Thu Jan 1 09:00:00 1970 @@ -1,24 +0,0 @@ ---- makefile.orig Thu Feb 13 15:17:25 2003 -+++ makefile Thu Feb 13 15:15:48 2003 -@@ -4,15 +4,15 @@ - rm *.o - - OBJECTS = interface.o sequence.o showpair.o malign.o \ -- util.o trees.o gcgcheck.o prfalign.o pairalign.o \ -- calcgapcoeff.o calcprf1.o calcprf2.o calctree.o \ -- readmat.o alnscore.o random.o -+ util.o trees.o gcgcheck.o prfalign.o pairalign.o \ -+ calcgapcoeff.o calcprf1.o calcprf2.o calctree.o \ -+ readmat.o alnscore.o random.o - - HEADERS = general.h clustalw.h - --CC = cc --CFLAGS = -c -O --LFLAGS = -O -lm -+CC ?= cc -+CFLAGS += -c -DDATADIR=\"${PREFIX}/share/clustalw\" -+LFLAGS = -lm - - clustalw : $(OBJECTS) amenu.o clustalw.o - $(CC) -o $@ $(OBJECTS) amenu.o clustalw.o $(LFLAGS) diff -ruN clustalw.orig/files/patch-ac clustalw/files/patch-ac --- clustalw.orig/files/patch-ac Thu Aug 28 13:51:02 2003 +++ clustalw/files/patch-ac Thu Jan 1 09:00:00 1970 @@ -1,137 +0,0 @@ ---- interface.c.orig Thu Feb 13 15:17:33 2003 -+++ interface.c Thu Feb 13 15:26:28 2003 -@@ -1132,7 +1132,7 @@ - /* added for File System Standards - Francois */ - path1=(char *)ckalloc((strlen(path)+64)*sizeof(char)); - strcpy(path1,path); -- strcat(path1,"/usr/share/clustalx:/usr/local/share/clustalx"); -+ strcat(path1,DATADIR); - - lf=(sint)strlen(fname); - deb=path1; -@@ -1224,7 +1224,7 @@ - if(strstr(temp, help_marker)){ - if(usemenu) { - fprintf(stdout,"\n"); -- getstr("Press [RETURN] to continue",lin2); -+ getstr("Press [RETURN] to continue",lin2,MAXLINE); - } - fclose(help_file); - return; -@@ -1236,7 +1236,7 @@ - if(usemenu) { - if(nlines >= PAGE_LEN) { - fprintf(stdout,"\n"); -- getstr("Press [RETURN] to continue or X to stop",lin2); -+ getstr("Press [RETURN] to continue or X to stop",lin2,MAXLINE); - if(toupper(*lin2) == 'X') { - fclose(help_file); - return; -@@ -1248,7 +1248,7 @@ - } - if(usemenu) { - fprintf(stdout,"\n"); -- getstr("Press [RETURN] to continue",lin2); -+ getstr("Press [RETURN] to continue",lin2,MAXLINE); - } - fclose(help_file); - } -@@ -1287,7 +1287,7 @@ - ++nlines; - if(nlines >= PAGE_LEN) { - fprintf(stdout,"\n"); -- getstr("Press [RETURN] to continue or X to stop",lin2); -+ getstr("Press [RETURN] to continue or X to stop",lin2,MAXLINE); - if(toupper(*lin2) == 'X') { - fclose(file); - return; -@@ -1298,7 +1298,7 @@ - } - fclose(file); - fprintf(stdout,"\n"); -- getstr("Press [RETURN] to continue",lin2); -+ getstr("Press [RETURN] to continue",lin2,MAXLINE); - } - - -@@ -1747,7 +1747,7 @@ - FILE *infile; - - if(usemenu) -- getstr("Enter name of the matrix file",lin2); -+ getstr("Enter name of the matrix file",lin2,MAXLINE); - else - strcpy(lin2,str); - -@@ -1773,7 +1773,7 @@ - FILE *infile; - - if(usemenu) -- getstr("Enter name of the matrix file",lin2); -+ getstr("Enter name of the matrix file",lin2,MAXLINE); - else - strcpy(lin2,str); - -@@ -2176,7 +2176,7 @@ - strcpy(local_prompt,"\n\nEnter new name to avoid overwriting "); - strcat(local_prompt," [%s]: "); - fprintf(stdout,local_prompt,file_name); -- gets(temp); -+ fgets(temp,FILENAMELEN+1,stdin); if(*temp != EOS) temp[strlen(temp)-1]=EOS; - if(*temp != EOS) strcpy(file_name,temp); - } - } -@@ -2184,7 +2184,7 @@ - strcpy(local_prompt,prompt); - strcat(local_prompt," [%s]: "); - fprintf(stdout,local_prompt,file_name); -- gets(temp); -+ fgets(temp,FILENAMELEN+1,stdin); if(*temp != EOS) temp[strlen(temp)-1]=EOS; - if(*temp != EOS) strcpy(file_name,temp); - } - -@@ -2385,7 +2385,7 @@ - if (usemenu) - fprintf(stdout,"\nUse the existing GUIDE TREE file, %s (y/n) ? [y]: ", - tree_name); -- gets(temp); -+ fgets(temp,MAXLINE,stdin); if(*temp != EOS) temp[strlen(temp)-1]=EOS; - if(*temp != 'n' && *temp != 'N') { - strcpy(phylip_name,tree_name); - use_tree = TRUE; -@@ -2617,7 +2617,7 @@ - - fprintf(stdout,"\nEnter a name for the guide tree file [%s]: ", - phylip_name); -- gets(temp); -+ fgets(temp,MAXLINE,stdin); if(*temp != EOS) temp[strlen(temp)-1]=EOS; - if(*temp != EOS) - strcpy(phylip_name,temp); - } -@@ -2719,7 +2719,7 @@ - #endif - fprintf(stdout,"\nUse the existing GUIDE TREE file for Profile 1, %s (y/n) ? [y]: ", - tree_name); -- gets(temp); -+ fgets(temp,MAXLINE,stdin); if(*temp != EOS) temp[strlen(temp)-1]=EOS; - if(*temp != 'n' && *temp != 'N') { - strcpy(p1_tree_name,tree_name); - use_tree1 = TRUE; -@@ -2745,7 +2745,7 @@ - #endif - fprintf(stdout,"\nUse the existing GUIDE TREE file for Profile 2, %s (y/n) ? [y]: ", - tree_name); -- gets(temp); -+ fgets(temp,MAXLINE,stdin); if(*temp != EOS) temp[strlen(temp)-1]=EOS; - if(*temp != 'n' && *temp != 'N') { - strcpy(p2_tree_name,tree_name); - use_tree2 = TRUE; -@@ -4203,7 +4203,7 @@ - if(usemenu) { - fprintf(stdout,"\nEnter a name for the parameter output file [%s]: ", - parname); -- gets(temp); -+ fgets(temp,FILENAMELEN+1,stdin); if(*temp != EOS) temp[strlen(temp)-1]=EOS; - if(*temp != EOS) - strcpy(parname,temp); - } diff -ruN clustalw.orig/files/patch-ae clustalw/files/patch-ae --- clustalw.orig/files/patch-ae Sun Feb 16 03:43:14 2003 +++ clustalw/files/patch-ae Thu Jan 1 09:00:00 1970 @@ -1,138 +0,0 @@ ---- amenu.c.orig Thu Feb 13 15:19:00 2003 -+++ amenu.c Thu Feb 13 15:21:10 2003 -@@ -13,7 +13,8 @@ - static jmp_buf jmpbuf; - #ifndef VMS - #ifndef AIX --#define BADSIG (void (*)())-1 -+/* #define BADSIG (void (*)())-1 */ -+#define BADSIG SIG_ERR - #endif - #endif - -@@ -184,7 +185,7 @@ - fprintf(stdout," H. HELP\n"); - fprintf(stdout," X. EXIT (leave program)\n\n\n"); - -- getstr("Your choice",lin1); -+ getstr("Your choice",lin1,MAXLINE); - - switch(toupper(*lin1)) { - case '1': seq_input(FALSE); -@@ -268,7 +269,7 @@ - fprintf(stdout," H. HELP\n"); - fprintf(stdout," or press [RETURN] to go back to main menu\n\n\n"); - -- getstr("Your choice",lin1); -+ getstr("Your choice",lin1,MAXLINE); - if(*lin1 == EOS) return; - - switch(toupper(*lin1)) -@@ -361,7 +362,7 @@ - fprintf(stdout," H. HELP\n"); - fprintf(stdout," or press [RETURN] to go back to main menu\n\n\n"); - -- getstr("Your choice",lin1); -+ getstr("Your choice",lin1,MAXLINE); - if(*lin1 == EOS) return; - - switch(toupper(*lin1)) -@@ -457,7 +458,7 @@ - fprintf(stdout,"\n\n"); - fprintf(stdout," H. HELP\n\n\n"); - -- getstr("Enter number (or [RETURN] to exit)",lin2); -+ getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE); - if( *lin2 == EOS) { - return; - } -@@ -533,7 +534,7 @@ - fprintf(stdout,"--\n"); - - -- getstr("\n\nEnter number (or [RETURN] to exit)",lin2); -+ getstr("\n\nEnter number (or [RETURN] to exit)",lin2,MAXLINE); - if(*lin2 == EOS) return(output_struct_penalties); - - switch(toupper(*lin2)) -@@ -602,7 +603,7 @@ - fprintf(stdout," H. HELP\n"); - fprintf(stdout," or press [RETURN] to go back to main menu\n\n\n"); - -- getstr("Your choice",lin1); -+ getstr("Your choice",lin1,MAXLINE); - if(*lin1 == EOS) return; - - switch(toupper(*lin1)) -@@ -677,7 +678,7 @@ - fprintf(stdout,"\n"); - fprintf(stdout," H. HELP\n\n\n"); - -- getstr("Enter number (or [RETURN] to exit)",lin2); -+ getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE); - if(*lin2 == EOS) return; - - switch(toupper(*lin2)) { -@@ -766,7 +767,7 @@ - fprintf(stdout,"\n"); - fprintf(stdout," H. HELP\n\n\n"); - -- getstr("Enter number (or [RETURN] to exit)",lin2); -+ getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE); - if(*lin2 == EOS) return; - - switch(toupper(*lin2)) { -@@ -907,7 +908,7 @@ - - fprintf(stdout," H. HELP\n\n\n"); - -- getstr("Enter number (or [RETURN] to exit)",lin2); -+ getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE); - if( *lin2 == EOS) { - if(dnaflag) { - dna_pw_go_penalty = pw_go_penalty; -@@ -1029,7 +1030,7 @@ - fprintf(stdout," 8. Protein Gap Parameters\n\n"); - fprintf(stdout," H. HELP\n\n\n"); - -- getstr("Enter number (or [RETURN] to exit)",lin2); -+ getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE); - - if(*lin2 == EOS) { - if(dnaflag) { -@@ -1122,7 +1123,7 @@ - fprintf(stdout," 5. Toggle End Gap Separation :%s\n\n",(!use_endgaps) ? "OFF" : "ON"); - fprintf(stdout," H. HELP\n\n\n"); - -- getstr("Enter number (or [RETURN] to exit)",lin2); -+ getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE); - - if(*lin2 == EOS) return; - -@@ -1136,7 +1137,7 @@ - case '3': - fprintf(stdout,"Hydrophilic Residues Currently: %s\n",hyd_residues); - -- getstr("Enter residues (or [RETURN] to quit)",lin1); -+ getstr("Enter residues (or [RETURN] to quit)",lin1,MAXLINE); - if (*lin1 != EOS) { - for (i=0;i<strlen(hyd_residues) && i<26;i++) { - c = lin1[i]; -@@ -1188,7 +1189,7 @@ - fprintf(stdout,"--\n"); - - -- getstr("\n\nEnter number (or [RETURN] to exit)",lin2); -+ getstr("\n\nEnter number (or [RETURN] to exit)",lin2,MAXLINE); - if(*lin2 == EOS) return(matn); - - i=toupper(*lin2)-'0'; -@@ -1223,7 +1224,7 @@ - fprintf(stdout,"\n%s\n",title); - strcpy(line,prompt); - strcat(line, "(y/n) ? [y]"); -- getstr(line,lin2); -+ getstr(line,lin2,80); - if ((*lin2 != 'n') && (*lin2 != 'N')) - return('y'); - else diff -ruN clustalw.orig/files/patch-af clustalw/files/patch-af --- clustalw.orig/files/patch-af Sun Feb 16 03:43:14 2003 +++ clustalw/files/patch-af Thu Jan 1 09:00:00 1970 @@ -1,11 +0,0 @@ ---- clustalw.h.orig Thu Feb 13 15:21:45 2003 -+++ clustalw.h Thu Feb 13 15:21:57 2003 -@@ -238,7 +238,7 @@ - char *blank_to_(char *str); - char *upstr(char *str); - char *lowstr(char *str); --void getstr(char *instr, char *outstr); -+void getstr(char *instr, char *outstr, int len); - double getreal(char *instr, double minx, double maxx, double def); - int getint(char *instr, int minx, int maxx, int def); - void do_system(void); diff -ruN clustalw.orig/files/patch-ah clustalw/files/patch-ah --- clustalw.orig/files/patch-ah Sun Feb 16 03:43:14 2003 +++ clustalw/files/patch-ah Thu Jan 1 09:00:00 1970 @@ -1,11 +0,0 @@ ---- sequence.c.orig Thu Feb 13 15:27:06 2003 -+++ sequence.c Thu Feb 13 15:27:37 2003 -@@ -924,7 +924,7 @@ - static Boolean dnaflag1; - - if(usemenu) -- getstr("Enter the name of the sequence file",line); -+ getstr("Enter the name of the sequence file",line,FILENAMELEN+1); - else - strcpy(line,seqname); - if(*line == EOS) return -1; diff -ruN clustalw.orig/files/patch-ai clustalw/files/patch-ai --- clustalw.orig/files/patch-ai Sun Feb 16 03:43:14 2003 +++ clustalw/files/patch-ai Thu Jan 1 09:00:00 1970 @@ -1,11 +0,0 @@ ---- trees.c.orig Thu Feb 13 15:52:06 2003 -+++ trees.c Thu Feb 13 16:19:08 2003 -@@ -1497,7 +1497,7 @@ - fprintf(stdout,"\n or 3) use the PHYLIP package."); - fprintf(stdout,"\n\n"); - if (usemenu) -- getstr("Press [RETURN] to continue",dummy); -+ getstr("Press [RETURN] to continue",dummy,10); - } - - diff -ruN clustalw.orig/files/patch-aj clustalw/files/patch-aj --- clustalw.orig/files/patch-aj Sun Feb 16 03:43:14 2003 +++ clustalw/files/patch-aj Thu Jan 1 09:00:00 1970 @@ -1,43 +0,0 @@ ---- util.c.orig Thu Feb 13 16:19:35 2003 -+++ util.c Thu Feb 13 16:21:40 2003 -@@ -171,10 +171,11 @@ - return str; - } - --void getstr(char *instr,char *outstr) -+void getstr(char *instr,char *outstr, int len) - { - fprintf(stdout,"%s: ",instr); -- gets(outstr); -+ fgets(outstr, len, stdin); -+ outstr[strlen(outstr)-1] = '\0'; - } - - double getreal(char *instr,double minx,double maxx,double def) -@@ -185,7 +186,7 @@ - - while(TRUE) { - fprintf(stdout,"%s (%.1f-%.1f) [%.1f]: ",instr,minx,maxx,def); -- gets(line); -+ fgets(line, MAXLINE, stdin); - status=sscanf(line,"%f",&ret); - if(status == EOF) return def; - if(ret>maxx) { -@@ -210,7 +211,7 @@ - while(TRUE) { - fprintf(stdout,"%s (%d..%d) [%d]: ", - instr,(pint)minx,(pint)maxx,(pint)def); -- gets(line); -+ fgets(line, MAXLINE, stdin); - status=sscanf(line,"%d",&ret); - if(status == EOF) return def; - if(ret>maxx) { -@@ -230,7 +231,7 @@ - { - char line[MAXLINE]; - -- getstr("\n\nEnter system command",line); -+ getstr("\n\nEnter system command",line,MAXLINE); - if(*line != EOS) - system(line); - fprintf(stdout,"\n\n"); diff -ruN clustalw.orig/files/patch-general::ClustalWResources.cpp clustalw/files/patch-general::ClustalWResources.cpp --- clustalw.orig/files/patch-general::ClustalWResources.cpp Thu Jan 1 09:00:00 1970 +++ clustalw/files/patch-general::ClustalWResources.cpp Wed Oct 31 17:40:14 2007 @@ -0,0 +1,11 @@ +--- general/ClustalWResources.cpp.orig Thu Jul 19 18:44:22 2007 ++++ general/ClustalWResources.cpp Wed Oct 31 17:39:01 2007 +@@ -33,7 +33,7 @@ + executablePath = "."; + + //installPath +- installPath = "."; ++ installPath = DATADIR; + char *env; + if ((env = getenv(CLUW_INSTALL_DIR)) != 0) + { diff -ruN clustalw.orig/files/patch-general::Utility.cpp clustalw/files/patch-general::Utility.cpp --- clustalw.orig/files/patch-general::Utility.cpp Thu Jan 1 09:00:00 1970 +++ clustalw/files/patch-general::Utility.cpp Wed Oct 31 17:21:26 2007 @@ -0,0 +1,20 @@ +--- general/Utility.cpp.orig Wed May 23 22:47:41 2007 ++++ general/Utility.cpp Wed Oct 31 17:19:21 2007 +@@ -144,7 +144,7 @@ + while (true) + { + fprintf(stdout, "%s (%.1f-%.1f) [%.1f]: ", instr, minx, maxx, def); +- gets(line); ++ fgets(line, 1024, stdin); + status = sscanf(line, "%f", &ret); + if (status == EOF) + { +@@ -181,7 +181,7 @@ + while (true) + { + fprintf(stdout, "%s (%d..%d) [%d]: ", instr, minx, maxx, def); +- gets(line); ++ fgets(line, 1024, stdin); + status = sscanf(line, "%d", &ret); + if (status == EOF) + { diff -ruN clustalw.orig/pkg-descr clustalw/pkg-descr --- clustalw.orig/pkg-descr Tue Oct 3 10:10:19 2000 +++ clustalw/pkg-descr Wed Oct 31 19:18:23 2007 @@ -1,24 +1,19 @@ CLUSTAL W Multiple Sequence Alignment Program -ClustalW was written by Des Higgins (now at University College, Cork, -Ireland) (des@chah.ucc.ie), Julie Thompson (julie@IGBMC.u-strasbg.fr), -Toby Gibson, (Gibson@EMBL-Heidelberg.DE), and Franc'ois Jeanmougin -(pingouin@igbmc.u-strasbg.fr). It is a complete rewrite and upgrade of -the Clustal and ClustalV packages. which were developed by Des -Higgins. New features include the ability to detect read different -input formats (NBRF/PIR, Fasta, EMBL/Swissprot); align old alignments; -produce phylogenetic trees after alignment (Neighbor Joining trees -with a bootstrap option); write different alignment formats (Clustal, -NBRF/PIR, GCG, PHYLIP); full command line interface. It is described -in the following papers: +Clustal W is a multiple alignment program for DNA or proteins. +Clustal W was written by Des Higgins (des@chah.ucc.ie), Julie Thompson +(julie@IGBMC.u-strasbg.fr), and Toby Gibson (Gibson@EMBL-Heidelberg.DE). +Version 2.0 has been completely rewritten in C++. +Original Paper: Thompson, J.D., D. G. Higgins and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680. +Tips: Higgins, D. G., J. D. Thompson, and T. J. Gibson. 1996. Using CLUSTAL for multiple sequence alignments. Methods in Enzymology 266: 383-402. -WWW: http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html +WWW: http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ diff -ruN clustalw.orig/pkg-plist clustalw/pkg-plist --- clustalw.orig/pkg-plist Mon Jul 10 12:17:40 2000 +++ clustalw/pkg-plist Wed Oct 31 17:58:38 2007 @@ -1,3 +1,4 @@ bin/clustalw +bin/clustalw2 share/clustalw/clustalw_help @dirrm share/clustalw >Release-Note: >Audit-Trail: >Unformatted:
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?200710311039.l9VAduRm080120>