Directory GDE/RAxML/

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westram 2023-08-11 13:40 Rev.: 19480

* reintegrates 'gde' into 'trunk'
* adds: log:branches/gde@19460:19479

196 lines of code changed in 14 files:

• GDE/RAxML: axml.c (+84 -90), axml.h (+2 -2), bipartitionList.c (+2), classify.c (+5 -6), evaluateGenericSpecial.c (+21 -3), evaluatePartialGenericSpecial.c (+1), fastDNAparsimony.c (+15 -19), globalVariables.h (+3 -3), leaveDropping.c (+15 -14), models.c (+12 -15), multiple.c (+7 -8), newviewGenericSpecial.c (+17 -3), searchAlgo.c (+2 -2), treeIO.c (+10 -14)

westram 2023-08-05 13:40 Rev.: 19446

* introduce {{{onlyC_flags}}}
- flags used for C compilation only.
- similar to {{{cxxflags}}} (references added).
- pass down onlyC_flags into AxML, CLUSTAL, CLUSTALW, FASTDNAML, FASTTREE, GL, MrBAYES, PHYLIP, PHYML*, RAxML, SINA(unused), SOURCE_TOOLS, SUPPORT, TOOLS, TREEGEN + TREEPUZZLE.
- set flags to {{{-Werror-implicit-function-declaration}}}
* error is only effective in a small part of these modules.
* TODO: need to activate warnings -> will activate the error as well.

1 lines of code changed in 1 file:

• GDE/RAxML: Makefile (+1 -1)

westram 2018-10-17 11:00 Rev.: 17478

* reintegrates 'svalues' into 'trunk'
- implements #614
* adds: log:branches/svalues@17357:17419,17428:17464,17469,17471:17477

1 lines of code changed in 1 file:

• GDE/RAxML: axml.c (+1 -1)

westram 2015-05-30 14:37 Rev.: 13845

- remove executable flag

0 lines of code changed in 18 files:

• GDE/RAxML: ancestralStates.c (-1), avxLikelihood.c (-1), classify.c (-1), compiler.h (-1), evaluateGenericSpecial.c (-1), evaluatePartialGenericSpecial.c (-1), fastDNAparsimony.c (-1), fastSearch.c (-1), gcc.h (-1), leaveDropping.c (-1), ll_alloc.c (-1), ll_asm.h (-1), ll_list.h (-1), makenewzGenericSpecial.c (-1), mem_alloc.c (-1), ming.h (-1), newviewGenericSpecial.c (-1), rogueEPA.c (-1)

westram 2013-11-03 17:22 Rev.: 11062

* stop using malloc.h

1 lines of code changed in 1 file:

• GDE/RAxML: Makefile (+1)

westram 2013-10-29 13:23 Rev.: 10955

- renamed
* ACC -> A_CC
* CPP -> A_CXX (misleading atm, since it contains c++flags)

1 lines of code changed in 1 file:

• GDE/RAxML: Makefile (+1 -1)

aboeckma 2013-08-06 12:58 Rev.: 10409

Updated raxml to current version

63097 lines of code changed in 44 files:

• GDE/RAxML: Makefile (+18 -13), Makefile.MPI (del), Makefile.PTHREADS (del), Makefile.PTHREADS.MAC (del), Makefile.gcc (del), RAxML-Manual.7.0.3.pdf (del), ancestralStates.c (new 999), avxLikelihood.c (new 4074), axml.c (+8358 -4335), axml.h (+1004 -433), bipartitionList.c (+4300 -969), categorizeGeneric.c (del), classify.c (new 2184), compiler.h (new 28), evaluateGeneric.c (del), evaluateGenericSpecial.c (new 3648), evaluateGenericVector.c (del), evaluatePartialGeneric.c (del), evaluatePartialGenericSpecial.c (new 1373), fastDNAparsimony.c (new 2631), fastSearch.c (new 1450), gcc.h (new 49), globalVariables.h (+146 -19), leaveDropping.c (new 1669), ll_alloc.c (new 6066), ll_asm.h (new 321), ll_list.h (new 145), makenewzGeneric.c (del), makenewzGenericSpecial.c (new 4737), mem_alloc.c (new 125), ming.h (new 109), models.c (+3400 -884), multiple.c (+1304 -2015), newviewGeneric.c (del), newviewGenericSpecial.c (new 8502), optimizeModel.c (+3233 -2148), parsePartitions.c (+660 -176), rapidBootstrap.c (+39 -43), raxmlParsimony.c (del), rev_functions.c (del), rogueEPA.c (new 422), searchAlgo.c (+528 -2203), topologies.c (+294 -386), treeIO.c (+1281 -832)

westram 2013-02-13 13:24 Rev.: 9575

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• GDE/RAxML: Makefile (+1 -1)

westram 2009-08-14 16:29 Rev.: 6141

* spellchecked all (phew)

1 lines of code changed in 1 file:

• GDE/RAxML: parsePartitions.c (+1 -1)

westram 2009-04-29 13:20 Rev.: 5872

* Changed variable transfer to sub-makefiles
- most variables are now exported via environment (using SOURCE_TOOLS/export2sub or AISC/export2sub)
- only variables that contain different values for different sub-makefile-calls are passed by cl (e.g. cflags, MAIN)
- changed flavour of exported variables (recursively expanded -> simply expanded variables). Please use VAR := VALUE in Makefiles (not VAR = VALUE). See http://www.gnu.org/software/make/manual/html_node/Flavors.html#Flavors for details
* removed/fixed all undefined variables in Makefiles (using 'make --warn-undefined-variables')
* changed names of compile-logs generated in GDE subdir
* added target 'xmlin' (broken, print warning)

1 lines of code changed in 1 file:

• GDE/RAxML: Makefile (+1 -1)

westram 2008-04-16 08:46 Rev.: 5262

- update to RAxML 7.0.3

6447 lines of code changed in 24 files:

• GDE/RAxML: Makefile.PTHREADS (+2 -2), Makefile.PTHREADS.MAC (new 50), Makefile.gcc (+1 -1), RAxML-Manual.7.0.0.pdf (del), RAxML-Manual.7.0.3.pdf (new 1), axml.c (+1314 -436), axml.h (+132 -40), bipartitionList.c (+28 -4), categorizeGeneric.c (+139 -138), evaluateGeneric.c (+243 -142), evaluateGenericVector.c (+132 -29), evaluatePartialGeneric.c (+196 -41), globalVariables.h (+2 -16), makenewzGeneric.c (+192 -179), models.c (+763 -645), multiple.c (+376 -145), newviewGeneric.c (+259 -79), optimizeModel.c (+329 -291), parsePartitions.c (+68 -4), rapidBootstrap.c (+15 -5), raxmlParsimony.c (+67 -64), searchAlgo.c (+1895 -118), topologies.c (+16 -60), treeIO.c (+227 -140)

westram 2008-02-15 19:20 Rev.: 5071

- depends updated

41 lines of code changed in 1 file:

• GDE/RAxML: Makefile (+41)

meierh 2008-01-22 13:14 Rev.: 5021

raxml7.0.0 introduce, RAxML5 removed

37908 lines of code changed in 39 files:

• GDE/RAxML: Makefile (+12 -26), Makefile.MPI (new 48), Makefile.PTHREADS (new 50), Makefile.gcc (new 48), RAxML-Manual.7.0.0.pdf (new 2203), README (del), Recommended_use.txt (del), axml.c (+5000 -11553), axml.h (+703 -243), bipartitionList.c (new 1326), categorizeGeneric.c (new 1285), cons.c (del), cons.h (del), consense.c (del), dnapars.c (del), evaluateGeneric.c (new 2382), evaluateGenericVector.c (new 1225), evaluatePartialGeneric.c (new 815), getopt.c (del), getopt.h (del), globalVariables.h (new 107), gpl.txt (del), makenewzGeneric.c (new 3119), models.c (new 1789), multiple.c (new 2310), newviewGeneric.c (new 5552), optimizeModel.c (new 2786), parsePartitions.c (new 922), phylip.c (del), phylip.h (del), phylip2.h (del), rapidBootstrap.c (new 437), raxmlParsimony.c (new 1814), rev_functions.c (+36 -7), searchAlgo.c (new 1630), softwaredisclaimer (del), topologies.c (new 761), treeIO.c (new 1548), unused_sources.tgz (del)

westram 2006-10-27 12:08 Rev.: 4210

- packed several unused files into .tgz

140 lines of code changed in 7 files:

• GDE/RAxML: Makefile.intel (del), Makefile.pgi (del), example_alignment (del), example_input_tree (del), example_weights (del), examples.exec (del), unused_sources.tgz (new 140)

westram 2005-11-03 19:40 Rev.: 3954

- Erste Anbindung von PGT an ARB

0 lines of code changed in 1 file:

• GDE/RAxML: Makefile (-8)

westram 2005-06-22 10:42 Rev.: 3934

- added prototype for tred2

2 lines of code changed in 1 file:

• GDE/RAxML: axml.h (+2)

westram 2005-06-22 10:42 Rev.: 3933

- C compilation error

2 lines of code changed in 1 file:

• GDE/RAxML: axml.c (+2 -3)

westram 2005-06-22 10:41 Rev.: 3932

- use C compiler again
- only build raxml objects

5 lines of code changed in 1 file:

• GDE/RAxML: Makefile (+5 -5)

westram 2005-06-22 09:55 Rev.: 3928

- use c++ compiler to compile raxml (not compiling!)

7 lines of code changed in 1 file:

• GDE/RAxML: Makefile (+7 -6)

artemov 2005-06-21 12:46 Rev.: 3927

*** empty log message ***

21745 lines of code changed in 23 files:

• GDE/RAxML: Makefile (new 83), Makefile.intel (new), Makefile.pgi (new), README (new 208), Recommended_use.txt (new 49), axml.c (new 12608), axml.h (new 405), cons.c (new 1240), cons.h (new 57), consense.c (new 607), dnapars.c (new 2448), example_alignment (new), example_input_tree (new), example_weights (new), examples.exec (new), getopt.c (new 116), getopt.h (new 14), gpl.txt (new 340), phylip.c (new 2600), phylip.h (new 596), phylip2.h (new 180), rev_functions.c (new 174), softwaredisclaimer (new 20)