Directory GDE/MUSCLE/src/

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westram 2020-10-19 11:14 Rev.: 18607

* partial merge from 'stable' into 'trunk'
* adds: [18606/branches/stable] (#830)

2 lines of code changed in 1 file:

• GDE/MUSCLE/src: subfams.cpp (+2 -2)

westram 2020-03-16 14:29 Rev.: 18388

* fix potential buffer overflow (warned by gcc 7.5.0).

1 lines of code changed in 1 file:

• GDE/MUSCLE/src: typetostr.cpp (+1 -1)

westram 2013-10-18 09:39 Rev.: 10835

* directly build $ARBHOME/bin/muscle
* fixed problematic subdir generation
1. create subdir if needed
2. recall make on target
* moved unused source files out of sight

0 lines of code changed in 3 files:

• GDE/MUSCLE/src: gatest.cpp (del), redblack.cpp (del), scoremx.cpp (del)

aboeckma 2013-08-07 10:29 Rev.: 10413

Make arb_srclist happy

0 lines of code changed in 2 files:

• GDE/MUSCLE/src: make.err (del), make.out (del)

aboeckma 2013-08-01 14:03 Rev.: 10392

remove binary

0 lines of code changed in 1 file:

• GDE/MUSCLE/src: muscle21 (del)

aboeckma 2013-08-01 14:02 Rev.: 10390

added muscle sourcles amd makefile

35265 lines of code changed in 196 files:

• GDE/MUSCLE/src: README.txt (new 27), aligngivenpath.cpp (new 802), aligngivenpathsw.cpp (new 237), aligntwomsas.cpp (new 41), aligntwoprofs.cpp (new 31), aln.cpp (new 170), alpha.cpp (new 283), alpha.h (new 106), anchors.cpp (new 218), bittraceback.cpp (new 206), blosum62.cpp (new 28), blosumla.cpp (new 118), clust.cpp (new 666), clust.h (new 148), cluster.cpp (new 339), cluster.h (new 86), clustset.h (new 21), clustsetdf.h (new 48), clustsetmsa.h (new 55), clwwt.cpp (new 190), color.cpp (new 189), cons.cpp (new 118), diaglist.cpp (new 378), diaglist.h (new 89), diffobjscore.cpp (new 162), diffpaths.cpp (new 114), difftrees.cpp (new 381), difftreese.cpp (new 235), distcalc.cpp (new 89), distcalc.h (new 45), distfunc.cpp (new 113), distfunc.h (new 36), distpwkimura.cpp (new 45), domuscle.cpp (new 299), dosp.cpp (new 60), dpregionlist.h (new 73), dpreglist.cpp (new 108), dpreglist.h (new 76), drawtree.cpp (new 41), edgelist.cpp (new 88), edgelist.h (new 28), enumopts.cpp (new 8), enumopts.h (new 16), enums.h (new 98), enumtostr.cpp (new 16), estring.cpp (new 689), estring.h (new 13), fasta.cpp (new 56), fasta2.cpp (new 114), fastclust.cpp (new 77), fastdist.cpp (new 56), fastdistjones.cpp (new 206), fastdistkbit.cpp (new 109), fastdistkmer.cpp (new 247), fastdistmafft.cpp (new 290), fastdistnuc.cpp (new 265), fastscorepath2.cpp (new 165), finddiags.cpp (new 161), finddiagsn.cpp (new 152), gapscoredimer.h (new 69), gatest.cpp (new), glbalign.cpp (new 165), glbalign352.cpp (new 55), glbaligndiag.cpp (new 172), glbalignla.cpp (new 432), glbalignle.cpp (new 435), glbalignns.cpp (new 374), glbalignsimple.cpp (new 368), glbalignsp.cpp (new 374), glbalignspn.cpp (new 409), glbalignss.cpp (new 318), glbalndimer.cpp (new 390), globals.cpp (new 289), globalslinux.cpp (new 163), globalsosx.cpp (new 92), globalsother.cpp (new 62), globalswin32.cpp (new 100), gonnet.cpp (new 499), gonnet.h (new 12), gotowt.cpp (new), henikoffweight.cpp (new 84), henikoffweightpb.cpp (new 124), html.cpp (new 136), hydro.cpp (new 42), intmath.cpp (new 354), intmath.h (new 210), local.cpp (new 100), main.cpp (new 72), make.err (new), make.out (new 2), makerootmsa.cpp (new 231), makerootmsab.cpp (new 62), maketree.cpp (new 38), mhack.cpp (new 64), mpam200.cpp (new 107), msa.cpp (new 851), msa.h (new 179), msa2.cpp (new 531), msadist.h (new 39), msadistkimura.cpp (new 88), msadistkimura.h (new 13), msadistmafft.h (new 24), msf.cpp (new 121), muscle.cpp (new 130), muscle.h (new 330), muscle21 (new), muscleout.cpp (new 116), nucmx.cpp (new 23), nwdasimple.cpp (new 494), nwdasimple2.cpp (new 549), nwdasmall.cpp (new 947), nwrec.cpp (new 137), nwsmall.cpp (new 664), objscore.cpp (new 113), objscore.h (new 30), objscore2.cpp (new 522), objscoreda.cpp (new 289), onexception.cpp (new 15), options.cpp (new 241), outweights.cpp (new 17), pam200mafft.cpp (new 32), params.cpp (new 631), params.h (new 118), phy.cpp (new 1130), phy2.cpp (new 282), phy3.cpp (new 469), phy4.cpp (new 295), phyfromclust.cpp (new 95), phyfromfile.cpp (new 272), physeq.cpp (new 128), phytofile.cpp (new 86), posgap.cpp (new 141), ppscore.cpp (new 93), profdb.cpp (new 54), profile.cpp (new 147), profile.h (new 126), profilefrommsa.cpp (new 318), progalign.cpp (new 206), progress.cpp (new 172), progressivealign.cpp (new 76), pwpath.cpp (new 386), pwpath.h (new 100), readmx.cpp (new 158), realigndiffs.cpp (new 115), realigndiffse.cpp (new 142), redblack.cpp (new 471), refine.cpp (new 80), refinehoriz.cpp (new 288), refinesubfams.cpp (new 212), refinetree.cpp (new 59), refinetreee.cpp (new 51), refinevert.cpp (new 159), refinew.cpp (new 227), releases.txt (new 13), savebest.cpp (new 66), scoredist.cpp (new 128), scoregaps.cpp (new 201), scorehistory.cpp (new 101), scorehistory.h (new 21), scoremx.cpp (new 45), scorepp.cpp (new 104), seq.cpp (new 342), seq.h (new 85), seqvect.cpp (new 290), seqvect.h (new 63), setblosumweights.cpp (new 131), setgscweights.cpp (new 195), setnewhandler.cpp (new 26), spfast.cpp (new 269), sptest.cpp (new 176), stabilize.cpp (new 21), subfam.cpp (new 409), subfams.cpp (new 65), svnmods.h (new 1), svnversion.h (new 1), sw.cpp (new 206), termgaps.cpp (new 36), textfile.cpp (new 359), textfile.h (new 70), threewaywt.cpp (new 342), timing.h (new 24), tomhydro.cpp (new 109), traceback.cpp (new 208), tracebackopt.cpp (new 73), tracebacksw.cpp (new 186), tree.h (new 339), treefrommsa.cpp (new 97), types.h (new 117), typetostr.cpp (new 58), unixio.h (new 11), upgma2.cpp (new 395), usage.cpp (new 44), validateids.cpp (new 112), version.txt (new 1), vtml2.cpp (new 145), writescorefile.cpp (new 69)