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commit 062ddf0e617fb3fbda4d2d9a387027fa8386b2e4 Merge: 2311c4c 6dce4f7 Author: Andreas Tille <[email protected]> Date: Tue Nov 14 10:52:24 2017 +0100 Update upstream source from tag 'upstream/2.1' Update to upstream version '2.1' with Debian dir bd8d0cfadb133505731f6a362c96ca102dc93a35 COPYING | 622 ++ INSTALL | 156 + Makefile.am | 19 + QuickStart.txt | 55 + README.txt | 156 + bootstrap.sh | 13 + build_garli.sh | 96 + config.h.in | 125 + config/acx_mpi.m4 | 181 + config/compile | 347 + config/config.guess | 1501 +++ config/config.sub | 1566 ++++ config/depcomp | 423 + config/install-sh | 251 + config/libtool.m4 | 7831 ++++++++++++++++ config/ltmain.sh | 9636 ++++++++++++++++++++ config/missing | 336 + configure.ac | 389 + doc/Garli0.96Manual.pdf | Bin 0 -> 228229 bytes doc/NOTE.txt | 4 + example/basic/EXAMPLES.txt | 46 + example/basic/LGmodel.mod | 92 + example/basic/garli.conf | 65 + example/basic/garli.conf.AA.LGmodel | 66 + example/basic/garli.conf.AA.defaultSettings | 65 + example/basic/garli.conf.AA.test | 66 + example/basic/garli.conf.codon.defaultSettings | 66 + example/basic/garli.conf.codon.test | 66 + example/basic/garli.conf.nuc.defaultSettings | 65 + example/basic/garli.conf.nuc.test | 65 + example/basic/rana.nex | 76 + example/basic/rana.phy | 65 + example/basic/ranaconstraint.format1 | 2 + example/basic/ranaconstraint.format2 | 2 + example/basic/ranastart.nexus.tre | 75 + example/basic/ranastart.oldformat.tre | 1 + example/basic/zakonEtAl2006.11tax.nex | 25 + example/partition/EXAMPLES.txt | 18 + .../3diffModels.byCodonPos.best.all.tre | 45 + .../3diffModels.byCodonPos.best.tre | 20 + .../3diffModels.byCodonPos.log00.log | 3980 ++++++++ .../3diffModels.byCodonPos.screen.log | 1450 +++ .../exampleRuns/3parts.diffModelTypes/garli.conf | 83 + .../3parts.diffModelTypes/zakonEtAl2006.11tax.nex | 32 + .../GTRG.byCodonPos.best.all.tre | 45 + .../3parts.sameModelType/GTRG.byCodonPos.best.tre | 20 + .../3parts.sameModelType/GTRG.byCodonPos.log00.log | 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241 + src/configreader.cpp | 640 ++ src/configreader.h | 87 + src/datamatr.cpp | 1946 ++++ src/datamatr.h | 517 ++ src/defs.h | 161 + src/errorexception.h | 125 + src/funcs.cpp | 1038 +++ src/funcs.h | 224 + src/garli.br | 87 + src/garlimain.cpp | 904 ++ src/garlireader.cpp | 1435 +++ src/garlireader.h | 236 + src/individual.cpp | 1054 +++ src/individual.h | 173 + src/linalg.cpp | 1363 +++ src/linalg.h | 22 + src/memchk.h | 325 + src/model.cpp | 4966 ++++++++++ src/model.h | 2199 +++++ src/mpifuncs.cpp | 1290 +++ src/mpifuncs.h | 82 + src/mpitrick.cpp | 287 + src/optimization.cpp | 3718 ++++++++ src/optimizationinfo.h | 88 + src/outputman.h | 343 + src/population.cpp | 7970 ++++++++++++++++ src/population.h | 590 ++ src/reconnode.h | 544 ++ src/rng.cpp | 659 ++ src/rng.h | 127 + src/sequencedata.cpp | 1579 ++++ src/sequencedata.h | 959 ++ src/set.cpp | 90 + src/set.h | 145 + src/stopwatch.h | 93 + src/threaddcls.h | 43 + src/threadfunc.cpp | 499 + src/translatetable.cpp | 89 + src/translatetable.h | 58 + src/tree.cpp | 8597 +++++++++++++++++ src/tree.h | 843 ++ src/treenode.cpp | 890 ++ src/treenode.h | 153 + src/utility.h | 323 + tests/Makefile.am | 3 + tests/check/a.G3.conf | 68 + tests/check/a.G4.conf | 67 + tests/check/a.conf | 66 + tests/check/c.M3x2.conf | 67 + tests/check/c.conf | 68 + tests/check/g.dnaBnoZ.conf | 76 + tests/check/g.dnaMix.conf | 76 + tests/check/n.G3.conf | 66 + tests/check/n.G4.conf | 66 + tests/check/n.conf | 66 + tests/check/n.const.conf | 66 + tests/check/p.3diff.conf | 83 + tests/check/p.mk.ssr.conf | 68 + tests/check/p.mkO.ssr.conf | 68 + tests/check/p.mkv.ssr.conf | 68 + tests/check/p.mkvO.ssr.conf | 68 + tests/const/n.neg.const.conf | 64 + tests/const/n.negBack.const.conf | 64 + tests/const/n.pos.const.conf | 65 + tests/const/n.posBack.const.conf | 65 + tests/data/L.start | 44 + tests/data/L2001.30x52.nex | 240 + tests/data/a.G3.start | 22 + tests/data/a.G4.start | 22 + tests/data/a.start | 17 + tests/data/c.M3x2.start | 21 + 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