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commit dd9c17c1dd2670d00c51c583a7daa12c677984b0 Merge: 6084400 9f4c57b Author: Kevin Murray <[email protected]> Date: Sat Feb 6 16:05:32 2016 +0100 Merge tag 'upstream/3.2.0+dfsg' Upstream version 3.2.0+dfsg .gitignore | 29 + LICENSE | 339 +++ README | 16 +- README.md | 6 + autogen.sh | 2 + config.h.in | 12 +- configure.ac | 29 +- confmc | 9 + confr | 9 + confrf | 9 + doc/example.html | 1331 ---------- doc/example.text | 2812 --------------------- doc/naturemag.bst | 3049 ++++++++++++----------- doc/phyml-manual.pdf | Bin 392421 -> 407931 bytes doc/phyml-manual.tex | 21 +- doc/ref.bib | 5534 +++++++++++++++++++++++++++++++++++++++++- examples/X1.mat | 21 - src/Makefile.am | 29 +- src/Makefile_mc.am | 39 + src/Makefile_r.am | 86 + src/alrt.c | 2 +- src/bionj.c | 14 +- src/bionj.h | 2 +- src/cl.c | 95 +- src/cl.h | 2 +- src/free.c | 72 +- src/free.h | 2 + src/geo.c | 1 - src/help.c | 5 +- src/init.c | 362 ++- src/init.h | 8 +- src/interface.c | 6 +- src/{sergeii.c => invitee.c} | 4 +- src/{sergeii.h => invitee.h} | 4 +- src/io.c | 590 +++-- src/io.h | 2 +- src/lk.c | 507 ++-- src/main.c | 58 +- src/make.c | 159 +- src/make.h | 9 +- src/mcmc.c | 4640 +++++++++++++++++++++++------------ src/mcmc.h | 47 +- src/mg.c | 2 +- src/migrep.c | 1819 -------------- src/migrep.h | 59 - src/mixt.c | 23 +- src/models.c | 106 +- src/mpi_boot.c | 4 +- src/mxml.h | 329 +++ src/nexus.c | 17 +- src/optimiz.c | 1163 ++++----- src/phyrex.c | 4173 +++++++++++++++++++++++++++++++ src/phyrex.h | 113 + src/rates.c | 4 +- src/simu.c | 42 +- src/spr.c | 12 +- src/stats.c | 980 +++++++- src/stats.h | 25 + src/times.c | 23 +- src/utilities.c | 921 ++++--- src/utilities.h | 167 +- src/xml.c | 10 +- version | 1 + 63 files changed, 18837 insertions(+), 11129 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/phyml.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
