Directory GDE/PHYLIP/

Lines of Code

Developers

Most Recent Commits

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

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

1289 lines of code changed in 49 files:

• GDE/PHYLIP: Makefile (+1 -36), clique.c (+44 -44), cons.c (+28 -26), cons.h (+1 -1), consense.c (+5 -5), contml.c (+10 -10), contrast.c (+12 -8), disc.c (+17 -17), discrete.c (+79 -81), dnacomp.c (+55 -50), dnaml.c (+48 -44), dnamlk.c (+53 -48), dnamove.c (+36 -31), dnapars.c (+29 -24), dnapenny.c (+1 -1), dollop.c (+36 -31), dolmove.c (+22 -17), dolpenny.c (+4 -4), draw.c (+105 -113), draw.h (+2 -3), draw2.c (+41 -52), drawgram.c (+35 -34), drawtree.c (+23 -27), factor.c (+24 -24), fitch.c (+17 -18), hermite.c (del), interface.c (del), interface.h (del), io.h (del), kitsch.c (+1 -1), macface.c (del), macface.h (del), mix.c (+23 -23), move.c (+31 -27), moves.c (+30 -30), neighbor.c (+5 -5), pars.c (+33 -25), penny.c (+2 -2), phylip.c (+43 -39), phylip.h (+2 -2), proml.c (+61 -56), promlk.c (+74 -73), protdist.c (+54 -54), protpars.c (+37 -37), restdist.c (+3 -8), restml.c (+20 -20), retree.c (+59 -60), seq.c (+80 -80), seqboot.c (+3 -1)

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.

47 lines of code changed in 1 file:

• GDE/PHYLIP: Makefile (+47 -46)

westram 2019-04-04 16:47 Rev.: 17742

* fix unnecessary typos.

2 lines of code changed in 2 files:

• GDE/PHYLIP: dnaml.c (+1 -1), dnamlk.c (+1 -1)

epruesse 2016-06-13 23:33 Rev.: 14934

Merge r14911:14914,r14933 -- additional path options for build system

- allow overriding X11 include/lib path from config.makefile
- add Makefile variables XML_INCLUDES and XAW_LIBS

Allows setting explicit paths for those libs by adding lines to
config.makefile like so:

export XLIBS=$(shell pkg-config --libs xpm xerces-c)
export XML_INCLUDES=$(shell pkg-config --cflags xerces-c)
export XAW_LIBS=$(shell pkg-config --libs xaw7)
------------------------------------------------------------------------

1 lines of code changed in 1 file:

• GDE/PHYLIP: Makefile (+1 -1)

westram 2015-01-23 15:19 Rev.: 13443

* reintegrates 'vectorize' into 'trunk'
- adds vectorization check for gcc 4.9.x / NDEBUG compile
* adds:
- log:branches/vectorize@13428:13442

1 lines of code changed in 1 file:

• GDE/PHYLIP: Makefile (+1 -1)

westram 2013-11-03 15:42 Rev.: 11060

* reintegrates 'ptsfix' into 'trunk':
* adds:
- log:branches/ptsdump@8966:9000
- log:branches/ptsfix@8965:9012,9014:9017,9019:9023,9025:9046,9048:9089,9091:9114,9116:9132,9134:9139,9141:9145,9147:9151,9153:9158,9160:9379,9381:11059
- log:branches/ptsstartup@9160:9235,9237:9278,9280:9336,9339:9361,9363:9446
- log:branches/ptsundef@9061:9358

1 lines of code changed in 1 file:

• GDE/PHYLIP: treedist.c (+1 -1)

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

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

46 lines of code changed in 1 file:

• GDE/PHYLIP: Makefile (+46 -46)

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

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• GDE/PHYLIP: Makefile (+1 -1)

westram 2010-09-18 17:20 Rev.: 6866

* compiler-messages (merges [6848] [6849] [6850] [6851] [6853] [6855] [6856] [6860] from refactor)
- errors get listed before warnings
- pipe all compilations through postcompile filter
- optionally filter warnings and/or stop at 1st error (controllable by POST_COMPILE in ARB Makefile)
- no warnings for ptpan (too many; version in trunk is outdated)

1 lines of code changed in 1 file:

• GDE/PHYLIP: Makefile (+1 -1)

westram 2009-04-19 19:36 Rev.: 5829

* included some patches for OSX (thx to Matt Cottrell)
* added global switch LINK_STATIC
* added script which checks for tools needed to compile ARB
* typo CCPLIB->CPPLIB

12 lines of code changed in 3 files:

• GDE/PHYLIP: protdist.c (+7 -2), seq.c (+3 -1), seq.h (+2)

baderk 2008-07-16 17:24 Rev.: 5458

Removed .cvsignore files from repository. Hopefully this time all svn:ignore flags were set right.

1 lines of code changed in 1 file:

• GDE/PHYLIP: hermite.c (+1 -1)

westram 2007-05-30 15:34 Rev.: 4634

- proper clean (avoid errors if already cleaned)

4 lines of code changed in 1 file:

• GDE/PHYLIP: Makefile (+4 -5)

westram 2004-01-23 19:08 Rev.: 2338

fixed and reformatted dependencies (using fix_depends.pl)

80 lines of code changed in 1 file:

• GDE/PHYLIP: Makefile (+80 -35)

westram 2003-11-23 14:43 Rev.: 2206

dependency update

14 lines of code changed in 1 file:

• GDE/PHYLIP: Makefile (+14 -4)

westram 2003-11-21 14:12 Rev.: 2183

- distinguish between EOF and EOL
- show partly read name in case of error

92 lines of code changed in 1 file:

• GDE/PHYLIP: phylip.c (+92 -82)

westram 2003-11-20 13:36 Rev.: 2175

upgrade to PHYLIP 3.6

54576 lines of code changed in 123 files:

• GDE/PHYLIP: Makefile (+173 -46), Makefile.qc (del), Makefile.tc (del), README (del), clique.c (+558 -824), clique.doc (del), compile.com (del), cons.c (new 1236), cons.h (new 57), consense.c (+272 -1259), consense.doc (del), cont.c (new 218), cont.h (new 19), contchar.doc (del), contml.c (+429 -989), contml.doc (del), contrast.c (+698 -563), contrast.doc (del), disc.c (new 926), disc.h (new 85), discrete.c (new 2931), discrete.doc (del), discrete.h (new 141), dist.c (new 454), dist.h (new 32), distance.doc (del), dnacomp.c (+571 -1732), dnacomp.doc (del), dnadist.c (+698 -769), dnadist.doc (del), dnainvar.c (+277 -602), dnainvar.doc (del), dnaml.c (+2105 -1024), dnaml.doc (del), dnaml2.c (del), dnamlk.c (+2215 -1013), dnamlk.doc (del), dnamlk2.c (del), dnamove.c (+714 -1115), dnamove.doc (del), dnapars.c (+1233 -1832), dnapars.doc (del), dnapenny.c (+377 -1496), dnapenny.doc (del), dollo.c (new 369), dollo.h (new 28), dollop.c (+428 -1526), dollop.doc (del), dolmove.c (+673 -1446), dolmove.doc (del), dolpenny.c (+325 -1292), dolpenny.doc (del), draw.c (new 3575), draw.doc (del), draw.h (new 179), draw2.c (new 1800), drawgram.c (+1088 -531), drawgram.doc (del), drawgraphics.c (del), drawgraphics.h (del), drawtree.c (+1993 -614), drawtree.doc (del), factor.c (+218 -310), factor.doc (del), fitch.c (+373 -1155), fitch.doc (del), font1 (del), font2 (del), font3 (del), font4 (del), font5 (del), font6 (del), gendist.c (+210 -305), gendist.doc (del), hermite.c (new 549), interface.c (+247 -484), interface.h (+36 -34), io.h (new 8), kitsch.c (+345 -929), kitsch.doc (del), macface.c (new 107), macface.h (new 27), main.doc (del), makeinf.c (del), makeinf.doc (del), mix.c (+896 -823), mix.doc (del), mix2.c (del), move.c (+691 -1577), move.doc (del), moves.c (new 293), moves.h (new 34), neighbor.c (+248 -746), neighbor.doc (del), pars.c (new 1582), penny.c (+405 -1510), penny.doc (del), phylip.c (new 2600), phylip.h (+461 -45), phylip.html (new 104), proml.c (new 2777), promlk.c (new 2905), protdist.c (+1181 -980), protdist.doc (del), protml.doc (del), protml.pas (del), protpars.c (+725 -1196), protpars.doc (del), restdist.c (new 633), restml.c (+1472 -680), restml.doc (del), restml2.c (del), retree.c (+2243 -1402), retree.doc (del), seq.c (new 3948), seq.h (new 208), seqboot.c (+614 -629), seqboot.doc (del), sequence.doc (del), treedist.c (new 992), vaxfix.c (del), wagner.c (new 535), wagner.h (new 32)

westram 2003-08-15 18:28 Rev.: 1731

- does not clear display

53 lines of code changed in 4 files:

• GDE/PHYLIP: consense.c (+9 -8), dnapars.c (+15 -14), protpars.c (+15 -14), seqboot.c (+14 -13)

westram 2003-08-09 14:00 Rev.: 1617

- updated dependencies for all Makefiles
- rewrote dependency generation code. Only real changes
propagate into Makefiles - so it does no longer hurt to
call 'make depends' in ARB directory!

69 lines of code changed in 1 file:

• GDE/PHYLIP: Makefile (+69 -375)

westram 2002-05-29 17:46 Rev.: 597

*** empty log message ***

372 lines of code changed in 1 file:

• GDE/PHYLIP: Makefile (+372 -31)

yadhu 2002-05-29 11:53 Rev.: 593

makefile dependency generation fixed for GDE

31 lines of code changed in 1 file:

• GDE/PHYLIP: Makefile (+31 -372)

westram 2002-05-23 09:29 Rev.: 566

Most changes are made due to activating more warnings for the c++ compiler (linux)

74 lines of code changed in 1 file:

• GDE/PHYLIP: Makefile (+74 -72)

jobb 2001-05-04 14:52 Rev.: 181

added new phylip version

81215 lines of code changed in 91 files:

• GDE/PHYLIP: Makefile (new 415), Makefile.qc (new 101), Makefile.tc (new 114), README (new 192), clique.c (new 1719), clique.doc (new 252), compile.com (new 100), consense.c (new 1399), consense.doc (new 252), contchar.doc (new 126), contml.c (new 1902), contml.doc (new 315), contrast.c (new 779), contrast.doc (new 189), discrete.doc (new 378), distance.doc (new 315), dnacomp.c (new 2299), dnacomp.doc (new 252), dnadist.c (new 1346), dnadist.doc (new 441), dnainvar.c (new 1127), dnainvar.doc (new 441), dnaml.c (new 1286), dnaml.doc (new 567), dnaml2.c (new 1435), dnamlk.c (new 1318), dnamlk.doc (new 567), dnamlk2.c (new 1569), dnamove.c (new 2277), dnamove.doc (new 315), dnapars.c (new 2230), dnapars.doc (new 252), dnapenny.c (new 1913), dnapenny.doc (new 819), dollop.c (new 2052), dollop.doc (new 315), dolmove.c (new 2342), dolmove.doc (new 378), dolpenny.c (new 1677), dolpenny.doc (new 567), draw.doc (new 693), drawgram.c (new 1003), drawgram.doc (new 252), drawgraphics.c (new 2205), drawgraphics.h (new 59), drawtree.c (new 1189), drawtree.doc (new 189), factor.c (new 646), factor.doc (new 315), fitch.c (new 1892), fitch.doc (new 189), font1 (new 193), font2 (new 301), font3 (new 396), font4 (new 293), font5 (new 399), font6 (new 370), gendist.c (new 462), gendist.doc (new 252), interface.c (new 538), interface.h (new 42), kitsch.c (new 1559), kitsch.doc (new 252), main.doc (new 4288), makeinf.c (new 682), makeinf.doc (new 355), mix.c (new 1046), mix.doc (new 378), mix2.c (new 1322), move.c (new 2483), move.doc (new 378), neighbor.c (new 1080), neighbor.doc (new 189), penny.c (new 1922), penny.doc (new 567), phylip.h (new 180), protdist.c (new 1608), protdist.doc (new 315), protml.doc (new 728), protml.pas (new 3509), protpars.c (new 2361), protpars.doc (new 378), restml.c (new 1060), restml.doc (new 441), restml2.c (new 1528), retree.c (new 2381), retree.doc (new 315), seqboot.c (new 956), seqboot.doc (new 315), sequence.doc (new 378), vaxfix.c (new 50)

jobb 2001-05-04 14:19 Rev.: 180

removed old phylip

0 lines of code changed in 46 files:

• GDE/PHYLIP: Makefile (del), clique.c (del), coallike.c (del), consense.c (del), contml.c (del), contrast.c (del), dnacomp.c (del), dnadist.c (del), dnainvar.c (del), dnaml.c (del), dnaml2.c (del), dnamlk.c (del), dnamlk2.c (del), dnamove.c (del), dnapars.c (del), dnapenny.c (del), dollop.c (del), dolmove.c (del), dolpenny.c (del), drawgram.c (del), drawgraphics.c (del), drawgraphics.h (del), drawtree.c (del), factor.c (del), fitch.c (del), gendist.c (del), interface.c (del), interface.h (del), kitsch.c (del), makeinf.c (del), mix.c (del), mix2.c (del), move.c (del), neighbor.c (del), p2c.h (del), p2clib.c (del), penny.c (del), phylip.h (del), protdist.c (del), protml.c (del), protpars.c (del), restml.c (del), restml2.c (del), retree.c (del), seqboot.c (del), vaxfix.c (del)

westram 2001-01-11 16:58 Rev.: 83

*** empty log message ***

383 lines of code changed in 1 file:

• GDE/PHYLIP: Makefile (+383 -486)

meierh 2001-01-11 16:24 Rev.: 80

haralds checkin

486 lines of code changed in 1 file:

• GDE/PHYLIP: Makefile (+486 -383)

westram 2001-01-04 16:36 Rev.: 68

Updated dependencies

309 lines of code changed in 1 file:

• GDE/PHYLIP: Makefile (+309 -82)

oldcode 2000-11-23 11:41 Rev.: 2

Initial revision

57112 lines of code changed in 46 files:

• GDE/PHYLIP: Makefile (new 188), clique.c (new 1719), coallike.c (new), consense.c (new 1399), contml.c (new 1902), contrast.c (new 779), dnacomp.c (new 2299), dnadist.c (new 1346), dnainvar.c (new 1127), dnaml.c (new 1286), dnaml2.c (new 1435), dnamlk.c (new 1318), dnamlk2.c (new 1569), dnamove.c (new 2277), dnapars.c (new 2230), dnapenny.c (new 1913), dollop.c (new 2052), dolmove.c (new 2342), dolpenny.c (new 1677), drawgram.c (new 1003), drawgraphics.c (new 2205), drawgraphics.h (new 59), drawtree.c (new 1189), factor.c (new 646), fitch.c (new 1892), gendist.c (new 462), interface.c (new 538), interface.h (new 42), kitsch.c (new 1559), makeinf.c (new 682), mix.c (new 1046), mix2.c (new 1322), move.c (new 2483), neighbor.c (new 1080), p2c.h (new), p2clib.c (new), penny.c (new 1922), phylip.h (new 180), protdist.c (new 1608), protml.c (new), protpars.c (new 2361), restml.c (new 1060), restml2.c (new 1528), retree.c (new 2381), seqboot.c (new 956), vaxfix.c (new 50)