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Searched refs:bionj (Results 1 – 8 of 8) sorted by relevance

/dports/biology/phyml/phyml-3.3.20200621/src/
H A DMakefile.am104 bionj.c bionj.h\
140 bionj.c bionj.h\
202 bionj.c bionj.h\
225 bionj.c bionj.h\
251 bionj.c bionj.h\
287 bionj.c bionj.h\
324 bionj.c bionj.h\
360 bionj.c bionj.h\
396 bionj.c bionj.h\
429 bionj.c bionj.h\
[all …]
H A DMakefile_r.am4 rwrapper_SOURCES = main.c utilities.c optimiz.c lk.c bionj.c models.c free.c\
6 rwrapper_LDADD = main.o utilities.o optimiz.o lk.o bionj.o models.o free.o\
36 bionj.o: bionj.c bionj.h
37 $(SCOMPILE) -c bionj.c
H A DMakefile_mc.am21 mc_SOURCES = main.c utilities.c optimiz.c lk.c bionj.c models.c free.c\
/dports/biology/seaview/seaview/
H A DMakefile43 …parser.o md5.o zsockr.o misc_acnuc.o dnapars.o protpars.o seq.o phylip.o lwl.o bionj.o phyml_util.o
H A Dtrees.cxx252 static Fl_Round_Button *bionj; in distance_method_dialog() local
269 bionj = new Fl_Round_Button(nj->x() + nj->w() + 10, nj->y(), nj->w(), nj->h(), "BioNJ"); in distance_method_dialog()
270 bionj->type(FL_RADIO_BUTTON); in distance_method_dialog()
271 …savetofile = new Fl_Round_Button(bionj->x() + bionj->w() + 10, nj->y(), 110, nj->h(), "Save to Fil… in distance_method_dialog()
304 bionj->setonly(); in distance_method_dialog()
343 if (usertree->value()) bionj->setonly(); in distance_method_dialog()
353 else if(o == usertree || o == nj || o == bionj || o == savetofile) { in distance_method_dialog()
380 … char *tree = run_distance_method(view, distance_choice, ignore_all_gaps->value(), bionj->value(), in distance_method_dialog()
384 const char *choice = bionj->value()? "BioNJ_tree" : "NJ_tree"; in distance_method_dialog()
/dports/biology/fasttree/FastTree-2.1.10_5/
H A DFastTree-2.1.10.c815 int bionj = 0; variable
1734 bionj = 0; in main()
1736 bionj = 1; in main()
1985 bionj ? "weighted" : "balanced" , in main()
2842 if (bionj && join.weight > 0.01 && varIJ > 0.001) { in FastNJ()
2924 bionj ? bionjWeight : /*noweight*/-1.0); in FastNJ()
6799 if (useML || !bionj) { in RecomputeProfile()
6837 if (!bionj) in QuartetWeight()
/dports/biology/phyml/phyml-3.3.20200621/doc/
H A Dphyml-manual.tex1646 \item \x{init.tree="bionj"|"user"|"random"}. Starting tree. Default is \x{bionj}.
1661 <instance id="T1" init.tree="bionj" optimise.tree="true" \
1928 <instance id="T1" init.tree="bionj" optimise.tree="yes" \
2078 <instance id="T1" init.tree="bionj" optimise.tree="yes" \
2154 <instance id="T1" init.tree="bionj" optimise.tree="yes" \
2371 <instance id="T1" init.tree="bionj" optimise.tree="yes"/>
/dports/biology/iqtree/IQ-TREE-2.0.6/tree/
H A Dphylotree.cpp3268 BioNj bionj; in computeBioNJ() local
3269 bionj.create(dist_file.c_str(), bionj_file.c_str()); in computeBioNJ()