[med-svn] [paml] branch master updated (8c7ab84 -> 99e336b)

Andreas Tille tille at debian.org
Thu Oct 6 03:57:23 UTC 2016 

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository paml.

      from  8c7ab84   Fix permissions
       new  4fa6da4   New upstream version 4.9c+dfsg
       new  4bef5d0   Merge tag 'upstream/4.9c+dfsg'
       new  99e336b   Upstream has released a new version mentioning GPL in some file but not all.  Need to clarify again

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 3s.trees                                           |   0
 4s.trees                                           |   0
 5s.trees                                           |   0
 6s.trees                                           |   0
 GeneticCode.txt                                    |   0
 MCaa.dat                                           |   0
 MCbase.dat                                         |   0
 MCbaseRandomTree.dat                               |   0
 MCcodon.dat                                        |   0
 README.txt                                         |   0
 Technical/Pt/testPMat.c                            |   0
 Technical/Simulation/Codon/MCcodonNSbranches.dat   |   0
 .../Simulation/Codon/MCcodonNSbranchsites.dat      |   0
 Technical/Simulation/Codon/MCcodonNSclade.dat      |   0
 Technical/Simulation/Codon/MCcodonNSsites.dat      |   0
 Technical/Simulation/Codon/PositiveSites.c         |   0
 Technical/Simulation/Codon/README.txt              |   0
 Technical/Simulation/Codon/codeml.ctl              |   0
 Technical/Simulation/multiruns.c                   |   0
 Technical/Simulation/multiruns.txt                 |   0
 aaml.ctl                                           |   0
 baseml.ctl                                         |   0
 brown.nuc                                          |   0
 brown.rooted.trees                                 |   0
 brown.trees                                        |   0
 codeml.ctl                                         |   0
 codonml.ctl                                        |   0
 dat/MtZoa.dat                                      |   0
 dat/cpREV10.dat                                    |   0
 dat/cpREV64.dat                                    |   0
 dat/dayhoff-dcmut.dat                              |   0
 dat/dayhoff.dat                                    |   0
 dat/g1974a.dat                                     |   0
 dat/g1974c.dat                                     |   0
 dat/g1974p.dat                                     |   0
 dat/g1974v.dat                                     |   0
 dat/grantham.dat                                   |   0
 dat/jones-dcmut.dat                                |   0
 dat/jones.dat                                      |   0
 dat/lg.dat                                         |   0
 dat/miyata.dat                                     |   0
 dat/mtArt.dat                                      |   0
 dat/mtREV24.dat                                    |   0
 dat/mtmam.dat                                      |   0
 dat/wag.dat                                        |   0
 debian/changelog                                   |   2 +-
 doc/pamlHistory.txt                                |  14 +++
 examples/9s.trees                                  |   0
 examples/CladeModelCD/ECP_EDN_15.nuc               |   0
 examples/CladeModelCD/codeml.CladeC.ctl            |   0
 examples/CladeModelCD/codeml.CladeD.ctl            |   0
 examples/CladeModelCD/tree.txt                     |   0
 examples/DatingSoftBound/FixedDsClock23.txt        |   0
 examples/DatingSoftBound/README.txt                |   0
 .../DatingSoftBound/mcmctree.Infinitesites.ctl     |   0
 examples/DatingSoftBound/mcmctree.ctl              |   0
 examples/DatingSoftBound/mtCDNApri.trees           |   0
 examples/DatingSoftBound/mtCDNApri123.txt          |   0
 examples/HIVNSsites/HIVenvSweden.trees             |   0
 examples/HIVNSsites/HIVenvSweden.txt               |   0
 examples/HIVNSsites/HIVenvSweden4s.trees           |   0
 examples/HIVNSsites/HIVenvSweden4s.txt             |   0
 examples/HIVNSsites/README.txt                     |   0
 examples/HIVNSsites/codeml.ctl                     |   0
 examples/MHC.Swanson2002MBE/README.txt             |   0
 examples/MHC.Swanson2002MBE/bigmhc.phy             |   0
 examples/MHC.Swanson2002MBE/bigmhc.trees           |   0
 examples/MHC.Swanson2002MBE/codeml.ctl             |   0
 examples/MouseLemurs/MouseLemurs.aa                |   0
 examples/MouseLemurs/MouseLemurs.nuc               |   0
 examples/MouseLemurs/MouseLemurs.trees             |   0
 examples/MouseLemurs/MouseLemurs123.nuc            |   0
 examples/MouseLemurs/README.txt                    |   0
 examples/MouseLemurs/README2.txt                   |   0
 examples/MouseLemurs/aaml.ctl                      |   0
 examples/MouseLemurs/aaml2.ctl                     |   0
 examples/MouseLemurs/baseml.ctl                    |   0
 examples/MouseLemurs/baseml2.ctl                   |   0
 examples/MouseLemurs/codeml.ctl                    |   0
 examples/MouseLemurs/codonml.ctl                   |   0
 examples/MouseLemurs/codonml2.ctl                  |   0
 examples/MouseLemurs/mtmam.dat                     |   0
 examples/README.txt                                |   0
 examples/TipDate.FluH1/H1.Beast.Nulldata.xml       |   0
 examples/TipDate.FluH1/H1.Beast.xml                |   0
 examples/TipDate.FluH1/H1.NodeNumbers.tre          |   0
 examples/TipDate.FluH1/H1.nexus                    |   0
 examples/TipDate.FluH1/H1.tre                      |   0
 examples/TipDate.FluH1/H1.txt                      |   0
 examples/TipDate.FluH1/baseml.ctl                  |   0
 examples/TipDate.FluH1/commands.txt                |   0
 examples/TipDate.FluH1/in.BV.HKYG5                 |   0
 examples/TipDate.FluH1/mcmctreeClock1.ctl          |   0
 examples/TipDate.FluH1/mcmctreeClock2.ctl          |   0
 examples/TipDate.FluH1/mcmctreeClock3.ctl          |   0
 examples/TipDate.HIV2/HIV2ge.tre                   |   0
 examples/TipDate.HIV2/HIV2ge.txt                   |   0
 examples/TipDate.HIV2/README.txt                   |   0
 examples/TipDate.HIV2/baseml.ctl                   |   0
 examples/TipDate.HIV2/in.BV.HKYG5                  |   0
 examples/TipDate.HIV2/mcmctree.ExactlnL.ctl        |   0
 examples/TipDate.HIV2/mcmctree.ctl                 |   0
 examples/YN00abglobin.result                       |   0
 examples/abglobin.aa                               |   0
 examples/abglobin.nuc                              |   0
 examples/abglobin.trees                            |   0
 examples/dNdSGene1.nuc                             |   0
 examples/horai.nuc                                 |   0
 examples/horai.trees                               |   0
 examples/lysin/README.txt                          |   0
 examples/lysin/RasMol.txt                          |   0
 examples/lysin/SiteNumbering.txt                   |   0
 examples/lysin/codeml.ctl                          |   0
 examples/lysin/codemlYangSwanson2002.ctl           |   0
 examples/lysin/lysin.nuc                           |   0
 examples/lysin/lysin.trees                         |   0
 examples/lysin/lysinYangSwanson2002.nuc            |   0
 examples/lysozyme/README.txt                       |   0
 examples/lysozyme/codeml.ctl                       |   4 +-
 examples/lysozyme/lysozymeLarge.ctl                |   0
 examples/lysozyme/lysozymeLarge.nuc                |   0
 examples/lysozyme/lysozymeLarge.trees              |   0
 examples/lysozyme/lysozymeSmall.ctl                |   0
 examples/lysozyme/lysozymeSmall.nuc                |   0
 examples/lysozyme/lysozymeSmall.trees              |   0
 examples/lysozyme/lysozymeSmall.txt                |   0
 examples/mtCDNA/README.txt                         |   0
 examples/mtCDNA/codeml.ctl                         |   0
 examples/mtCDNA/miyata.dat                         |   0
 examples/mtCDNA/mtCDNAmam.nuc                      |   0
 examples/mtCDNA/mtCDNAmam.trees                    |   0
 examples/mtCDNA/mtCDNApri.aa                       |   0
 examples/mtCDNA/mtCDNApri.nuc                      |   0
 examples/mtCDNA/mtCDNApri.trees                    |   0
 examples/mtCDNAape/2s.trees                        |   0
 examples/mtCDNAape/OmegaAA.dat                     |   0
 examples/mtCDNAape/README.txt                      |   0
 examples/mtCDNAape/codeml.HC.ctl                   |   0
 examples/mtCDNAape/codeml.ctl                      |   2 +-
 examples/mtCDNAape/mtCDNA.HC.txt                   |   0
 examples/mtCDNAape/mtCDNAape.trees                 |   0
 examples/mtCDNAape/mtCDNAape.txt                   |   0
 examples/mtprim9.nuc                               |   0
 mcmctree.ctl                                       |   0
 pamp.ctl                                           |   0
 paupblock                                          |   0
 paupend                                            |   0
 paupstart                                          |   0
 src/Makefile                                       |   0
 src/Makefile.MSVC                                  |   0
 src/README.txt                                     |  11 +-
 src/TreeTimeJeff.c                                 |   0
 src/baseml.c                                       |   0
 src/basemlg.c                                      |   0
 src/chi2.c                                         |   0
 src/codeml.c                                       |  25 ++---
 src/ds.c                                           |   0
 src/evolver.c                                      |   0
 src/mcmctree.c                                     |   0
 src/paml.h                                         |   5 +-
 src/pamp.c                                         |   0
 src/tools.c                                        | 117 ++++++++++++---------
 src/treespace.c                                    |   0
 src/treesub.c                                      | 111 ++++++++++++-------
 src/yn00.c                                         |   0
 stewart.aa                                         |   0
 stewart.trees                                      |   0
 yn00.ctl                                           |   0
 168 files changed, 181 insertions(+), 110 deletions(-)
 mode change 100755 => 100644 3s.trees
 mode change 100755 => 100644 4s.trees
 mode change 100755 => 100644 5s.trees
 mode change 100755 => 100644 6s.trees
 mode change 100755 => 100644 GeneticCode.txt
 mode change 100755 => 100644 MCaa.dat
 mode change 100755 => 100644 MCbase.dat
 mode change 100755 => 100644 MCbaseRandomTree.dat
 mode change 100755 => 100644 MCcodon.dat
 mode change 100755 => 100644 README.txt
 mode change 100755 => 100644 Technical/Pt/testPMat.c
 mode change 100755 => 100644 Technical/Simulation/Codon/MCcodonNSbranches.dat
 mode change 100755 => 100644 Technical/Simulation/Codon/MCcodonNSbranchsites.dat
 mode change 100755 => 100644 Technical/Simulation/Codon/MCcodonNSclade.dat
 mode change 100755 => 100644 Technical/Simulation/Codon/MCcodonNSsites.dat
 mode change 100755 => 100644 Technical/Simulation/Codon/PositiveSites.c
 mode change 100755 => 100644 Technical/Simulation/Codon/README.txt
 mode change 100755 => 100644 Technical/Simulation/Codon/codeml.ctl
 mode change 100755 => 100644 Technical/Simulation/multiruns.c
 mode change 100755 => 100644 Technical/Simulation/multiruns.txt
 mode change 100755 => 100644 aaml.ctl
 mode change 100755 => 100644 baseml.ctl
 mode change 100755 => 100644 brown.nuc
 mode change 100755 => 100644 brown.rooted.trees
 mode change 100755 => 100644 brown.trees
 mode change 100755 => 100644 codeml.ctl
 mode change 100755 => 100644 codonml.ctl
 mode change 100755 => 100644 dat/MtZoa.dat
 mode change 100755 => 100644 dat/cpREV10.dat
 mode change 100755 => 100644 dat/cpREV64.dat
 mode change 100755 => 100644 dat/dayhoff-dcmut.dat
 mode change 100755 => 100644 dat/dayhoff.dat
 mode change 100755 => 100644 dat/g1974a.dat
 mode change 100755 => 100644 dat/g1974c.dat
 mode change 100755 => 100644 dat/g1974p.dat
 mode change 100755 => 100644 dat/g1974v.dat
 mode change 100755 => 100644 dat/grantham.dat
 mode change 100755 => 100644 dat/jones-dcmut.dat
 mode change 100755 => 100644 dat/jones.dat
 mode change 100755 => 100644 dat/lg.dat
 mode change 100755 => 100644 dat/miyata.dat
 mode change 100755 => 100644 dat/mtArt.dat
 mode change 100755 => 100644 dat/mtREV24.dat
 mode change 100755 => 100644 dat/mtmam.dat
 mode change 100755 => 100644 dat/wag.dat
 mode change 100755 => 100644 examples/9s.trees
 mode change 100755 => 100644 examples/CladeModelCD/ECP_EDN_15.nuc
 mode change 100755 => 100644 examples/CladeModelCD/codeml.CladeC.ctl
 mode change 100755 => 100644 examples/CladeModelCD/codeml.CladeD.ctl
 mode change 100755 => 100644 examples/CladeModelCD/tree.txt
 mode change 100755 => 100644 examples/DatingSoftBound/FixedDsClock23.txt
 mode change 100755 => 100644 examples/DatingSoftBound/README.txt
 mode change 100755 => 100644 examples/DatingSoftBound/mcmctree.Infinitesites.ctl
 mode change 100755 => 100644 examples/DatingSoftBound/mcmctree.ctl
 mode change 100755 => 100644 examples/DatingSoftBound/mtCDNApri.trees
 mode change 100755 => 100644 examples/DatingSoftBound/mtCDNApri123.txt
 mode change 100755 => 100644 examples/HIVNSsites/HIVenvSweden.trees
 mode change 100755 => 100644 examples/HIVNSsites/HIVenvSweden.txt
 mode change 100755 => 100644 examples/HIVNSsites/HIVenvSweden4s.trees
 mode change 100755 => 100644 examples/HIVNSsites/HIVenvSweden4s.txt
 mode change 100755 => 100644 examples/HIVNSsites/README.txt
 mode change 100755 => 100644 examples/HIVNSsites/codeml.ctl
 mode change 100755 => 100644 examples/MHC.Swanson2002MBE/README.txt
 mode change 100755 => 100644 examples/MHC.Swanson2002MBE/bigmhc.phy
 mode change 100755 => 100644 examples/MHC.Swanson2002MBE/bigmhc.trees
 mode change 100755 => 100644 examples/MHC.Swanson2002MBE/codeml.ctl
 mode change 100755 => 100644 examples/MouseLemurs/MouseLemurs.aa
 mode change 100755 => 100644 examples/MouseLemurs/MouseLemurs.nuc
 mode change 100755 => 100644 examples/MouseLemurs/MouseLemurs.trees
 mode change 100755 => 100644 examples/MouseLemurs/MouseLemurs123.nuc
 mode change 100755 => 100644 examples/MouseLemurs/README.txt
 mode change 100755 => 100644 examples/MouseLemurs/README2.txt
 mode change 100755 => 100644 examples/MouseLemurs/aaml.ctl
 mode change 100755 => 100644 examples/MouseLemurs/aaml2.ctl
 mode change 100755 => 100644 examples/MouseLemurs/baseml.ctl
 mode change 100755 => 100644 examples/MouseLemurs/baseml2.ctl
 mode change 100755 => 100644 examples/MouseLemurs/codeml.ctl
 mode change 100755 => 100644 examples/MouseLemurs/codonml.ctl
 mode change 100755 => 100644 examples/MouseLemurs/codonml2.ctl
 mode change 100755 => 100644 examples/MouseLemurs/mtmam.dat
 mode change 100755 => 100644 examples/README.txt
 mode change 100755 => 100644 examples/TipDate.FluH1/H1.Beast.Nulldata.xml
 mode change 100755 => 100644 examples/TipDate.FluH1/H1.Beast.xml
 mode change 100755 => 100644 examples/TipDate.FluH1/H1.NodeNumbers.tre
 mode change 100755 => 100644 examples/TipDate.FluH1/H1.nexus
 mode change 100755 => 100644 examples/TipDate.FluH1/H1.tre
 mode change 100755 => 100644 examples/TipDate.FluH1/H1.txt
 mode change 100755 => 100644 examples/TipDate.FluH1/baseml.ctl
 mode change 100755 => 100644 examples/TipDate.FluH1/commands.txt
 mode change 100755 => 100644 examples/TipDate.FluH1/in.BV.HKYG5
 mode change 100755 => 100644 examples/TipDate.FluH1/mcmctreeClock1.ctl
 mode change 100755 => 100644 examples/TipDate.FluH1/mcmctreeClock2.ctl
 mode change 100755 => 100644 examples/TipDate.FluH1/mcmctreeClock3.ctl
 mode change 100755 => 100644 examples/TipDate.HIV2/HIV2ge.tre
 mode change 100755 => 100644 examples/TipDate.HIV2/HIV2ge.txt
 mode change 100755 => 100644 examples/TipDate.HIV2/README.txt
 mode change 100755 => 100644 examples/TipDate.HIV2/baseml.ctl
 mode change 100755 => 100644 examples/TipDate.HIV2/in.BV.HKYG5
 mode change 100755 => 100644 examples/TipDate.HIV2/mcmctree.ExactlnL.ctl
 mode change 100755 => 100644 examples/TipDate.HIV2/mcmctree.ctl
 mode change 100755 => 100644 examples/YN00abglobin.result
 mode change 100755 => 100644 examples/abglobin.aa
 mode change 100755 => 100644 examples/abglobin.nuc
 mode change 100755 => 100644 examples/abglobin.trees
 mode change 100755 => 100644 examples/dNdSGene1.nuc
 mode change 100755 => 100644 examples/horai.nuc
 mode change 100755 => 100644 examples/horai.trees
 mode change 100755 => 100644 examples/lysin/README.txt
 mode change 100755 => 100644 examples/lysin/RasMol.txt
 mode change 100755 => 100644 examples/lysin/SiteNumbering.txt
 mode change 100755 => 100644 examples/lysin/codeml.ctl
 mode change 100755 => 100644 examples/lysin/codemlYangSwanson2002.ctl
 mode change 100755 => 100644 examples/lysin/lysin.nuc
 mode change 100755 => 100644 examples/lysin/lysin.trees
 mode change 100755 => 100644 examples/lysin/lysinYangSwanson2002.nuc
 mode change 100755 => 100644 examples/lysozyme/README.txt
 mode change 100755 => 100644 examples/lysozyme/codeml.ctl
 mode change 100755 => 100644 examples/lysozyme/lysozymeLarge.ctl
 mode change 100755 => 100644 examples/lysozyme/lysozymeLarge.nuc
 mode change 100755 => 100644 examples/lysozyme/lysozymeLarge.trees
 mode change 100755 => 100644 examples/lysozyme/lysozymeSmall.ctl
 mode change 100755 => 100644 examples/lysozyme/lysozymeSmall.nuc
 mode change 100755 => 100644 examples/lysozyme/lysozymeSmall.trees
 mode change 100755 => 100644 examples/lysozyme/lysozymeSmall.txt
 mode change 100755 => 100644 examples/mtCDNA/README.txt
 mode change 100755 => 100644 examples/mtCDNA/codeml.ctl
 mode change 100755 => 100644 examples/mtCDNA/miyata.dat
 mode change 100755 => 100644 examples/mtCDNA/mtCDNAmam.nuc
 mode change 100755 => 100644 examples/mtCDNA/mtCDNAmam.trees
 mode change 100755 => 100644 examples/mtCDNA/mtCDNApri.aa
 mode change 100755 => 100644 examples/mtCDNA/mtCDNApri.nuc
 mode change 100755 => 100644 examples/mtCDNA/mtCDNApri.trees
 mode change 100755 => 100644 examples/mtCDNAape/2s.trees
 mode change 100755 => 100644 examples/mtCDNAape/OmegaAA.dat
 mode change 100755 => 100644 examples/mtCDNAape/README.txt
 mode change 100755 => 100644 examples/mtCDNAape/codeml.HC.ctl
 mode change 100755 => 100644 examples/mtCDNAape/codeml.ctl
 mode change 100755 => 100644 examples/mtCDNAape/mtCDNA.HC.txt
 mode change 100755 => 100644 examples/mtCDNAape/mtCDNAape.trees
 mode change 100755 => 100644 examples/mtCDNAape/mtCDNAape.txt
 mode change 100755 => 100644 examples/mtprim9.nuc
 mode change 100755 => 100644 mcmctree.ctl
 mode change 100755 => 100644 pamp.ctl
 mode change 100755 => 100644 paupblock
 mode change 100755 => 100644 paupend
 mode change 100755 => 100644 paupstart
 mode change 100755 => 100644 src/Makefile
 mode change 100755 => 100644 src/Makefile.MSVC
 mode change 100755 => 100644 src/README.txt
 mode change 100755 => 100644 src/TreeTimeJeff.c
 mode change 100755 => 100644 src/baseml.c
 mode change 100755 => 100644 src/basemlg.c
 mode change 100755 => 100644 src/chi2.c
 mode change 100755 => 100644 src/codeml.c
 mode change 100755 => 100644 src/ds.c
 mode change 100755 => 100644 src/evolver.c
 mode change 100755 => 100644 src/mcmctree.c
 mode change 100755 => 100644 src/paml.h
 mode change 100755 => 100644 src/pamp.c
 mode change 100755 => 100644 src/tools.c
 mode change 100755 => 100644 src/treespace.c
 mode change 100755 => 100644 src/treesub.c
 mode change 100755 => 100644 src/yn00.c
 mode change 100755 => 100644 stewart.aa
 mode change 100755 => 100644 stewart.trees
 mode change 100755 => 100644 yn00.ctl

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