Moved from treesoft.sf.net SVN

ACKNOWLEDGEMENTS

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+
+The following people contribute in some way to phylotree project. As we have
+not asked for their permission when making the list, we did not write their
+e-mail address here. Nonetheless, we really appreciate their generous
+contributions.
+
+Lachlan James Coin
+ For his beneficial discussion with constrained Neighbour-joining and various
+ tree-building algorithms.
+
+Richard Durbin
+ For his sparkling idea about TreeFam project and good instruction on tree-
+ cutting and constrained method. Without him, there will never be TreeBeST.
+
+Li Ruiqiang, Jean-Karim Heriche and Avril Coghlan
+ For their beneficial discussion and encouragement all the time.
+

AUTHORS

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+
+Li Heng, lh3@sanger.ac.uk, was the original author and chief programmer of
+treebest.
+
+Du Wenfeng, duwf@genomics.org.cn, was the author of dn/ds calculator. His
+creative idea accelerated the calculation speed by far.
+
+Guan Liang, guanl@genomics.org.cn, was the author of nh2pic, a wonderful
+NHX->FIGURE convertor. Although I do not use his codes any longer, I still
+appreciate his contribution to TreeBeST.
+
+Liu Tao, liutao@genomics.org.cn, was the author of goTree.pl, a wapper for
+the famous `puzzle' and `phyml' tree-builder.
+

ChangeLog

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+------------------------------------------------------------------------
+r274 | lh3lh3 | 2007-10-19 09:44:45 +0100 (Fri, 19 Oct 2007) | 3 lines
+
+ * 1.9.1-4
+ * rename project name as treebest
+
+------------------------------------------------------------------------
+r273 | lh3lh3 | 2007-10-19 09:17:05 +0100 (Fri, 19 Oct 2007) | 2 lines
+
+rename njtree to treebest
+
+------------------------------------------------------------------------
+r204 | lh3lh3 | 2007-01-29 10:04:07 +0000 (Mon, 29 Jan 2007) | 2 lines
+
+there is a bug in this tree.
+
+------------------------------------------------------------------------
+r197 | lh3lh3 | 2007-01-23 13:04:47 +0000 (Tue, 23 Jan 2007) | 2 lines
+
+add species trees for Ensembl
+
+------------------------------------------------------------------------
+r188 | lh3lh3 | 2007-01-18 10:53:36 +0000 (Thu, 18 Jan 2007) | 2 lines
+
+Makefiles for building universal binaries on Intel-Mac
+
+------------------------------------------------------------------------
+r186 | lh3lh3 | 2007-01-17 12:53:37 +0000 (Wed, 17 Jan 2007) | 8 lines
+
+
+ - add quiet mode to "njtree best"
+ - fix a bug in phyml when protein alignemnt is bootstrapped.
+ - add "fltk-config --post" for flnjtree under Mac OS X
+ - fix a typo in spec.*
+ - add taxon_id species tree
+
+
+------------------------------------------------------------------------
+r163 | lh3lh3 | 2006-12-04 08:53:49 +0000 (Mon, 04 Dec 2006) | 2 lines
+
+fix a bug when "njtree nj -s spec.nh" is in use.
+
+------------------------------------------------------------------------
+r153 | lh3lh3 | 2006-11-30 13:51:05 +0000 (Thu, 30 Nov 2006) | 2 lines
+
+my own branch
+
+------------------------------------------------------------------------
+r58 | lh3lh3 | 2006-10-26 08:48:56 +0100 (Thu, 26 Oct 2006) | 3 lines
+
+Add "trimpoor" which is expected to trim sequences that affect the quality of a
+gene trees. However, this has not been tested thoroughly.
+
+------------------------------------------------------------------------
+r53 | lh3lh3 | 2006-10-25 11:34:40 +0100 (Wed, 25 Oct 2006) | 4 lines
+
+
+ - fix a bug when packaging
+ - release 1.9.1
+
+------------------------------------------------------------------------
+r51 | lh3lh3 | 2006-10-24 15:23:38 +0100 (Tue, 24 Oct 2006) | 7 lines
+
+
+ - add SIS (species intersection score) for duplication nodes
+ - :DD=Y now means: Dubious Duplication. Previously it means
+   "confirmed duplication".
+ - fix a potential bug, although seemingly it has never happened.
+
+
+------------------------------------------------------------------------
+r20 | lh3lh3 | 2006-10-11 09:44:08 +0100 (Wed, 11 Oct 2006) | 2 lines
+
+Remove some obsolete rules
+
+------------------------------------------------------------------------
+r16 | lh3lh3 | 2006-10-10 13:58:05 +0100 (Tue, 10 Oct 2006) | 2 lines
+
+improve packaging method
+
+------------------------------------------------------------------------
+r15 | lh3lh3 | 2006-10-10 13:06:55 +0100 (Tue, 10 Oct 2006) | 2 lines
+
+change NJTREE version number
+
+------------------------------------------------------------------------
+r13 | lh3lh3 | 2006-10-10 11:57:54 +0100 (Tue, 10 Oct 2006) | 3 lines
+
+create dev branch
+
+
+------------------------------------------------------------------------
+r12 | lh3lh3 | 2006-10-10 10:48:55 +0100 (Tue, 10 Oct 2006) | 2 lines
+
+add njtree source codes.
+
+------------------------------------------------------------------------

FUTURES

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+
+HIGH Piority:
+
+
+MODERATE Piority:
+
+*  constrained NJ for multifurcated unrooted trees
+
+
+LOW Piority:
+
+*  Fetch TreeFam data via http connection. I am conceiving of some kind of
+   http library.
+*  Add more evolutionary model.
+
+
+Useful:
+
+*  Add a graphical multialignment viewer?
+

INSTALL

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+
+Just type `make', `treebest' will be compiled. If `FLTK' package has
+been installed, `make fltreebest' will generate the GUI version
+`fltreebest'. Please contact Heng Li <lh3@sanger.ac.uk> if you meet any
+problems.
+
+Good luck!
+

Makefile

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+CC=			gcc
+CXX=		g++
+CFLAGS=		-g -Wall -O2 -fomit-frame-pointer #-pg
+CXXFLAGS=	$(CFLAGS)
+YFLAGS= 
+DFLAGS=		-DUSE_GCC -DHAVE_PHYML -DLH3_ADDON # for phyml
+VERSION=	1.9.2
+NJVERSION=	-DTR_VERSION="\"$(VERSION)\"" -DTR_BUILD=\"`date +%d%b%Y`\"
+LEX=		flex
+YACC=		bison --yacc
+FLUID=		fluid
+FLTKCFG=	fltk-config
+PROG=		treebest
+LIBOBJS=	lex.yy.o y.tab.o read.o nj.o utils1.o subtree.o sdi.o bs_nj.o \
+			reroot.o task.o output.o ortho.o cut_tree.o spec.o utils2.o \
+			align.o filter.o aln_mask.o prob_dist.o brent.o ng86_ds.o lost.o \
+			tree_plot.o cpp_utils.o read_aln.o pre_cons.o simulate.o compare.o \
+			order.o nhx_output.o nj2.o backtrans.o phyml.o mmerge.o est_len.o \
+			best.o trimpoor.o
+FLOBJS=		flnjtree.o flnjtree_ui.o flglobal.o flworkspace.o flcallback.o
+INCLUDES=	-I.
+LIBS=		-L. -lphylotree -Lalign_lib -lalign -lm -Lphyml -lphyml
+SUBDIRS=	. align_lib phyml
+
+.SUFFIXES:.c .o .cc
+
+.c.o:
+		$(CC) -c $(DFLAGS) $(CFLAGS) $(INCLUDES) $< -o $@
+
+.cc.o:
+		$(CXX) -c $(DFLAGS) $(CXXFLAGS) $(INCLUDES) $< -o $@
+
+all:$(PROG)
+
+lib-recur all-recur clean-recur install-recur:
+		@target=`echo $@ | sed s/-recur//`; \
+		wdir=`pwd`; \
+		list='$(SUBDIRS)'; for subdir in $$list; do \
+			cd $$subdir; \
+			$(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+				INCLUDES="$(INCLUDES)" $$target || exit 1; \
+			cd $$wdir; \
+		done;
+
+lib:libphylotree.a
+
+libphylotree.a:$(LIBOBJS)
+		$(AR) -cru $@ $(LIBOBJS)
+
+treebest:lib-recur main.o
+		$(CXX) $(CFLAGS) $(DFLAGS) main.o -o $@ $(LIBS)
+
+fltreebest:lib-recur $(FLOBJS)
+		$(CXX) $(CXXFLAGS) $(DFLAGS) -o $@ $(FLOBJS) `$(FLTKCFG) --cxxflags` `$(FLTKCFG) --ldstaticflags` $(LIBS); \
+		$(FLTKCFG) --post $@
+
+timeout:timeout.o
+		$(CC) $(CFLAGS) $(DFLAGS) timeout.o -o $@
+
+make_ng86:make_ng86.o 
+		$(CC) $(CFLAGS) $(DFLAGS) make_ng86.o -o $@
+
+ng86_ds.h:make_ng86
+		./make_ng86 $@
+
+ng86_ds.o:ng86_ds.h ng86_ds.c
+
+main.o:main.c
+		$(CC) -c $(CFLAGS) $(DFLAGS) $(NJVERSION) main.c -o $@
+
+tags:*.c *.cc phyml/*.c align_lib/*.c phyml/*.cc
+		ctags *.c *.cc *.l *.y phyml/*.c phyml/*.cc align_lib/*.c common/*.h common/*.c
+
+treebest.pdf:treebest.texi
+		texi2pdf treebest.texi
+
+y.tab.c y.tab.h:parser.y
+		$(YACC) -d $(YFLAGS) parser.y
+
+lex.yy.c:parser.l
+		$(LEX) parser.l
+
+order.o:algo.h
+
+lex.yy.o:lex.yy.c y.tab.h
+		$(CC) -c $(DFLAGS) $(CFLAGS) lex.yy.c -o $@
+
+y.tab.cc:y.tab.c
+		ln -sf y.tab.c y.tab.cc
+
+y.tab.o:y.tab.cc
+		$(CXX) -c $(DFLAGS) $(CFLAGS) y.tab.cc -o $@
+
+set:
+		@if [ `expr match "$(DFLAGS_SPEC)" ".*HAVE_PHYML.*"` -ne 0 ]; then echo 'yes'; fi
+
+$(FLOBJS):flnjtree_ui.h flglobal.h
+flnjtree_ui.cc flnjtree_ui.h:flnjtree_ui.fl
+		$(FLUID) -c flnjtree_ui.fl
+
+package:lex.yy.c y.tab.c
+		@(cd ..; mv treebest treebest-$(VERSION); \
+			(find treebest-$(VERSION) -type f | grep -v "\.svn" | xargs tar cf -) | gzip > treebest-$(VERSION).tar.gz; \
+			mv treebest-$(VERSION) treebest)
+
+clean:
+		rm -f gmon.out *.o a.out y.output libphylotree.a *.cp *.fn *.ky *.pg *.tp *.vr *.toc *.aux *.pdf *.log \
+			treebest fltreebest timeout nh2pic flnjtree_ui.cc flnjtree_ui.h make_ng86 \
+			treebest-*.tar.bz2 ChangeLog.bak _phyml_boot*.txt \
+			y.tab.cc tags common/*.o treebest-*.tar.gz *~
+
+cleanmore:clean
+		rm -f ng86_ds.h lex.yy.c y.tab.*
+
+distclean:clean-recur
+		rm -f ng86_ds.h lex.yy.c y.tab.*

Makefile.mac

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+CC=			gcc
+CXX=		g++
+CFLAGS=		-Wall -O2 -fomit-frame-pointer -arch i386 -arch ppc #-pg
+CXXFLAGS=	$(CFLAGS)
+YFLAGS= 
+DFLAGS=		-DUSE_GCC -DHAVE_PHYML -DLH3_ADDON # for phyml
+VERSION=	1.9.2
+NJVERSION=	-DTR_VERSION="\"$(VERSION)\"" -DTR_BUILD=\"`date +%d%b%Y`\"
+LEX=		flex
+YACC=		bison --yacc
+FLUID=		fluid
+FLTKCFG=	fltk-config
+PROG=		treebest
+LIBOBJS=	lex.yy.o y.tab.o read.o nj.o utils1.o subtree.o sdi.o bs_nj.o \
+			reroot.o task.o output.o ortho.o cut_tree.o spec.o utils2.o \
+			align.o filter.o aln_mask.o prob_dist.o brent.o ng86_ds.o lost.o \
+			tree_plot.o cpp_utils.o read_aln.o pre_cons.o simulate.o compare.o \
+			order.o nhx_output.o nj2.o backtrans.o phyml.o mmerge.o est_len.o \
+			best.o trimpoor.o
+FLOBJS=		flnjtree.o flnjtree_ui.o flglobal.o flworkspace.o flcallback.o
+INCLUDES=	-I.
+LIBS=		-L. -lphylotree -Lalign_lib -lalign -lm -Lphyml -lphyml
+SUBDIRS=	. align_lib phyml
+
+.SUFFIXES:.c .o .cc
+
+.c.o:
+		$(CC) -c $(DFLAGS) $(CFLAGS) $(INCLUDES) $< -o $@
+
+.cc.o:
+		$(CXX) -c $(DFLAGS) $(CXXFLAGS) $(INCLUDES) $< -o $@
+
+all:$(PROG)
+
+lib-recur all-recur clean-recur install-recur:
+		@target=`echo $@ | sed s/-recur//`; \
+		wdir=`pwd`; \
+		list='$(SUBDIRS)'; for subdir in $$list; do \
+			cd $$subdir; \
+			$(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+				INCLUDES="$(INCLUDES)" $$target -f Makefile.mac || exit 1; \
+			cd $$wdir; \
+		done;
+
+lib:libphylotree.a
+
+libphylotree.a:$(LIBOBJS)
+		libtool -static -o $@ $(LIBOBJS)
+
+treebest:lib-recur main.o
+		$(CXX) $(CFLAGS) $(DFLAGS) main.o -o $@ $(LIBS)
+
+fltreebest:lib-recur $(FLOBJS)
+		$(CXX) $(CXXFLAGS) $(DFLAGS) -o $@ $(FLOBJS) `$(FLTKCFG) --cxxflags` `$(FLTKCFG) --ldstaticflags` $(LIBS); \
+		$(FLTKCFG) --post $@
+
+timeout:timeout.o
+		$(CC) $(CFLAGS) $(DFLAGS) timeout.o -o $@
+
+make_ng86:make_ng86.o 
+		$(CC) $(CFLAGS) $(DFLAGS) make_ng86.o -o $@
+
+ng86_ds.h:make_ng86
+		./make_ng86 $@
+
+ng86_ds.o:ng86_ds.h ng86_ds.c
+
+main.o:main.c
+		$(CC) -c $(CFLAGS) $(DFLAGS) $(NJVERSION) main.c -o $@
+
+tags:*.c *.cc phyml/*.c align_lib/*.c phyml/*.cc
+		ctags *.c *.cc *.l *.y phyml/*.c phyml/*.cc align_lib/*.c common/*.h common/*.c
+
+treebest.pdf:treebest.texi
+		texi2pdf treebest.texi
+
+y.tab.c y.tab.h:parser.y
+		$(YACC) -d $(YFLAGS) parser.y
+
+lex.yy.c:parser.l
+		$(LEX) parser.l
+
+order.o:algo.h
+
+lex.yy.o:lex.yy.c y.tab.h
+		$(CC) -c $(DFLAGS) $(CFLAGS) lex.yy.c -o $@
+
+y.tab.cc:y.tab.c
+		ln -sf y.tab.c y.tab.cc
+
+y.tab.o:y.tab.cc
+		$(CXX) -c $(DFLAGS) $(CFLAGS) y.tab.cc -o $@
+
+set:
+		@if [ `expr match "$(DFLAGS_SPEC)" ".*HAVE_PHYML.*"` -ne 0 ]; then echo 'yes'; fi
+
+$(FLOBJS):flnjtree_ui.h flglobal.h
+flnjtree_ui.cc flnjtree_ui.h:flnjtree_ui.fl
+		$(FLUID) -c flnjtree_ui.fl
+
+package:lex.yy.c y.tab.c
+		@(cd ..; mv treebest treebest-$(VERSION); \
+			(find treebest-$(VERSION) -type f | grep -v "\.svn" | xargs tar cf -) | gzip > treebest-$(VERSION).tar.gz; \
+			mv treebest-$(VERSION) treebest)
+
+clean:
+		rm -f gmon.out *.o a.out y.output libphylotree.a *.cp *.fn *.ky *.pg *.tp *.vr *.toc *.aux *.pdf *.log \
+			treebest fltreebest timeout nh2pic flnjtree_ui.cc flnjtree_ui.h make_ng86 fltreebest-*.tar.bz2 \
+			ChangeLog.bak _phyml_boot*.txt \
+			y.tab.cc tags common/*.o treebest-*.tar.gz *~
+
+cleanmore:clean
+		rm -f ng86_ds.h lex.yy.c y.tab.*
+
+distclean:clean-recur
+		rm -f ng86_ds.h lex.yy.c y.tab.*