/trunk Developers: aboeckma

Login name:
aboeckma
Total Commits:
803 (1.7%)
Lines of Code:
515,532 (20.8%)
Most Recent Commit:
2013-08-15 12:48
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Activity in Directories

Directory Changes Lines of Code Lines per Change
Totals 803 (100.0%) 515532 (100.0%) 642.0
GDE/MrBAYES/mrbayes_3.2.1/ 30 (3.7%) 114472 (22.2%) 3815.7
GDE/PHYML20130708/phyml/src/ 68 (8.5%) 78797 (15.3%) 1158.7
GDE/MAFFT/mafft-7.055-with-extensions/core/ 90 (11.2%) 75600 (14.7%) 840.0
GDE/RAxML/ 44 (5.5%) 63097 (12.2%) 1434.0
GDE/MAFFT/mafft-7.053-without-extensions/core/ 178 (22.2%) 53084 (10.3%) 298.2
GDE/MUSCLE/src/ 199 (24.8%) 35265 (6.8%) 177.2
GDE/PHYML20130708/phyml/doc/ 17 (2.1%) 24532 (4.8%) 1443.0
GDE/PHYML20130708/phyml/ 17 (2.1%) 22757 (4.4%) 1338.6
GDE/MAFFT/mafft-7.055-with-extensions/extensions/mxscarna_src/vienna/ 6 (0.7%) 11842 (2.3%) 1973.6
GDE/FASTTREE/ 2 (0.2%) 10116 (2.0%) 5058.0
GDE/MAFFT/mafft-7.055-with-extensions/extensions/mxscarna_src/probconsRNA/ 20 (2.5%) 7594 (1.5%) 379.7
GDE/MAFFT/mafft-7.055-with-extensions/extensions/mxscarna_src/ 21 (2.6%) 6910 (1.3%) 329.0
GDE/PROBCONS/probcons/ 21 (2.6%) 6318 (1.2%) 300.8
GDE/MAFFT/mafft-7.053-without-extensions/scripts/ 4 (0.5%) 2033 (0.4%) 508.2
GDE/PHYML20130708/phyml/examples/ 5 (0.6%) 1255 (0.2%) 251.0
GDEHELP/MENUS/ 16 (2.0%) 605 (0.1%) 37.8
GDEHELP/HELP_WRITTEN/ 4 (0.5%) 382 (0.1%) 95.5
GDE/MAFFT/mafft-7.055-with-extensions/ 7 (0.9%) 309 (0.1%) 44.1
GDE/PHYML20130708/phyml/examples/lg4x/ 5 (0.6%) 142 (0.0%) 28.4
GDE/MAFFT/mafft-7.055-with-extensions/extensions/ 2 (0.2%) 71 (0.0%) 35.5
GDE/MAFFT/mafft-7.053-without-extensions/ 6 (0.7%) 48 (0.0%) 8.0
GDE/MUSCLE/ 4 (0.5%) 40 (0.0%) 10.0
SH/ 2 (0.2%) 39 (0.0%) 19.5
GDE/PHYML20130708/ 2 (0.2%) 38 (0.0%) 19.0
GDE/MAFFT/ 3 (0.4%) 36 (0.0%) 12.0
WINDOW/ 1 (0.1%) 28 (0.0%) 28.0
GDE/MrBAYES/ 1 (0.1%) 26 (0.0%) 26.0
GDE/PROBCONS/ 1 (0.1%) 21 (0.0%) 21.0
UNIT_TESTER/ 4 (0.5%) 16 (0.0%) 4.0
GENOM/ 2 (0.2%) 12 (0.0%) 6.0
SL/DB_UI/ 1 (0.1%) 11 (0.0%) 11.0
bin/ 1 (0.1%) 9 (0.0%) 9.0
SOURCE_TOOLS/ 4 (0.5%) 8 (0.0%) 2.0
GDE/ 7 (0.9%) 7 (0.0%) 1.0
/ 2 (0.2%) 5 (0.0%) 2.5
util/ 3 (0.4%) 4 (0.0%) 1.3
GDE/PHYML20130708/phyml/bin/ 2 (0.2%) 2 (0.0%) 1.0
SL/TREE_READ/ 1 (0.1%) 1 (0.0%) 1.0

Activity of aboeckma

Most Recent Commits

aboeckma 2013-08-15 12:48 Rev.: 10456

Added rudimentary fasttree menu (need to know which options to use)

41 lines of code changed in 2 files:

  • GDE: Makefile (+1)
  • GDEHELP/MENUS: puzzle.menu (+40)
aboeckma 2013-08-15 11:37 Rev.: 10455

Added !MrBayes custom command file menu

75 lines of code changed in 2 files:

  • GDEHELP/HELP_WRITTEN: MrBayesCustom.help (new 44)
  • GDEHELP/MENUS: puzzle.menu (+31)
aboeckma 2013-08-15 10:12 Rev.: 10454

Added !MrBayes help

99 lines of code changed in 2 files:

  • GDEHELP/HELP_WRITTEN: MrBayes.help (new 97)
  • GDEHELP/MENUS: puzzle.menu (+2)
aboeckma 2013-08-14 15:35 Rev.: 10448

mafft changed default value for offset

7 lines of code changed in 1 file:

  • GDEHELP/MENUS: align.menu (+7 -6)
aboeckma 2013-08-14 15:28 Rev.: 10447

Added mrBayes gde menu

114 lines of code changed in 2 files:

  • GDEHELP/MENUS: puzzle.menu (+80)
  • SH: arb_nexus2newick.awk (new 34)
aboeckma 2013-08-14 15:27 Rev.: 10446

mafft preserve case

1 lines of code changed in 1 file:

  • GDEHELP/MENUS: align.menu (+1 -1)
aboeckma 2013-08-14 15:09 Rev.: 10445

Allow numbers with positive exponent in newick tree

1 lines of code changed in 1 file:

  • SL/TREE_READ: TreeRead.cxx (+1 -1)
aboeckma 2013-08-13 12:06 Rev.: 10435

Ignore tabs in !FastTree

1 lines of code changed in 1 file:

  • SOURCE_TOOLS: tabBrake.pl (+1)
aboeckma 2013-08-13 11:35 Rev.: 10433

Added fasttree2 source (no menu, yet)

10116 lines of code changed in 2 files:

  • GDE/FASTTREE: FastTree.c (new 10094), Makefile (new 22)
aboeckma 2013-08-13 11:01 Rev.: 10432

Added two missing switches to phyml

54 lines of code changed in 1 file:

  • GDEHELP/MENUS: phylip_ml.menu (+54 -31)
aboeckma 2013-08-13 11:00 Rev.: 10431

Added nbproject to arb_srclist ignore

1 lines of code changed in 1 file:

  • util: arb_srclst.pl (+1)
aboeckma 2013-08-08 14:40 Rev.: 10421

Fixed bug in mafft makefile

5 lines of code changed in 2 files:

  • GDE/MAFFT: Makefile (+3)
  • GDE/MAFFT/mafft-7.055-with-extensions/core: Makefile (+2 -3)
aboeckma 2013-08-07 14:47 Rev.: 10416

Added mr bayes (no menu yet)

114499 lines of code changed in 32 files:

  • GDE: Makefile (+1)
  • GDE/MrBAYES: Makefile (new 26)
  • GDE/MrBAYES/mrbayes_3.2.1: Makefile (new 30), bayes.c (new 1279), bayes.h (new 5), best.c (new 1875), best.h (new 37), command.c (new 15231), command.h (new 25), config.h (new 49), globals.h (new 211), gpl.txt (new 280), mb.c (new 2), mb.h (new 1431), mbbeagle.c (new 1262), mbbeagle.h (new 19), mbmath.c (new 5595), mbmath.h (new 56), mcmc.c (new 45903), mcmc.h (new 94), model.c (new 22464), model.h (new 53), plot.c (new 352), plot.h (new 2), sump.c (new 2874), sump.h (new 38), sumt.c (new 5753), sumt.h (new 9), tree.c (new 7473), tree.h (new 103), utils.c (new 1885), utils.h (new 82)
aboeckma 2013-08-07 11:29 Rev.: 10413

Make arb_srclist happy

1 lines of code changed in 4 files:

  • GDE/MUSCLE/src: make.err (del), make.out (del)
  • GDE/PROBCONS/probcons: VERSION (del)
  • util: arb_srclst.pl (+1 -1)
aboeckma 2013-08-07 11:25 Rev.: 10412

Removed muscle version file. Cannot make it work with arb_srclist

2 lines of code changed in 2 files:

  • GDE/MUSCLE: VERSION (del)
  • util: arb_srclst.pl (+2)
aboeckma 2013-08-07 11:03 Rev.: 10411

make probcons compile on linux (added cstring include )

3 lines of code changed in 3 files:

  • GDE/PROBCONS/probcons: CompareToRef.cc (+1), Main.cc (+1), ProjectPairwise.cc (+1)
aboeckma 2013-08-07 10:51 Rev.: 10410

Ignore probcons in tab break check

1 lines of code changed in 1 file:

  • SOURCE_TOOLS: tabBrake.pl (+1)
aboeckma 2013-08-06 12:58 Rev.: 10409

Updated raxml to current version

63104 lines of code changed in 46 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)
  • GDEHELP/MENUS: raxml.menu (+2 -6)
  • SH: arb_raxml (+5 -5)
aboeckma 2013-08-06 11:41 Rev.: 10408

Moved PROBCONS to NO_DEPENDS section.

1 lines of code changed in 1 file:

  • GDE: Makefile (+1 -1)
aboeckma 2013-08-02 11:45 Rev.: 10407

integrated probcons

47 lines of code changed in 1 file:

  • GDEHELP/MENUS: align.menu (+47)

(24 more)

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