[med-svn] [r-cran-ape] 01/05: Update debian/*

[Dylan Aïssi]

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bob.dybian-guest pushed a commit to branch master
in repository r-cran-ape.

commit 9c921baaa75aad7f3340d62ce8785f9cbfd25df5
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Sat Dec 3 23:21:10 2016 +0100

    Update debian/*
---
 debian/README.source     | 10 +---------
 debian/control           | 25 +++++++++++++------------
 debian/copyright         |  2 +-
 debian/upstream/metadata | 10 ++++++++++
 4 files changed, 25 insertions(+), 22 deletions(-)

diff --git a/debian/README.source b/debian/README.source
index 9f3e253..14b641b 100644
--- a/debian/README.source
+++ b/debian/README.source
@@ -37,10 +37,6 @@ Files: ape/data/HP.links.rda
 Documentation: man/parafit.Rd
   -> experiment data
 
-Files: ape/data/landplants.newick.rda
-Documentation: man/landplants.Rd
-  -> experiment data
-
 Files: ape/data/lice.D.rda
 Documentation: man/parafit.Rd
   -> experiment data
@@ -65,14 +61,10 @@ Files: ape/data/mat5Mrand.RData
 Documentation: man/mat5Mrand.Rd
   -> experiment data
 
-Files: ape/data/opsin.newick.rda
-Documentation: man/opsin.Rd
-  -> experiment data
-
 Files: ape/data/woodmouse.rda
 Documentation: man/woodmouse.Rd
   -> experiment data
 
 
- -- Dylan Aïssi <bob.dybian at gmail.com>  Sat, 10 May 2014 09:31:14 +0200
+ -- Dylan Aïssi <bob.dybian at gmail.com>  Sat, 03 Dec 2016 22:57:54 +0100
 
diff --git a/debian/control b/debian/control
index 49d94e3..7544c9d 100644
--- a/debian/control
+++ b/debian/control
@@ -29,15 +29,16 @@ Description: GNU R package for Analyses of Phylogenetics and Evolution
  This package provides functions for reading, writing, plotting, and
  manipulating phylogenetic trees, analyses of comparative data in a
  phylogenetic framework, ancestral character analyses, analyses of
- diversification and macroevolution, computing distances from allelic
- and nucleotide data, reading and writing nucleotide sequences as
- well as importing from BioConductor, and several tools such as
- Mantel's test, generalized skyline plots, graphical exploration of
- phylogenetic data (alex, trex, kronoviz), estimation of absolute
- evolutionary rates and clock-like trees using mean path lengths and
- penalized likelihood. Phylogeny estimation can be done with the NJ,
- BIONJ, ME, MVR, SDM, and triangle methods, and several methods
- handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the
- corresponding triangle method). Some functions call external
- applications (PhyML, Clustal, T-Coffee, Muscle) whose results are
- returned into R.
+ diversification and macroevolution, computing distances from DNA
+ sequences, reading and writing nucleotide sequences as well as
+ importing from BioConductor, and several tools such as Mantel's test,
+ generalized skyline plots, graphical exploration of phylogenetic data
+ (alex, trex, kronoviz), estimation of absolute evolutionary rates and
+ clock-like trees using mean path lengths and penalized likelihood,
+ dating trees with non-contemporaneous sequences, translating DNA into
+ AA sequences, and assessing sequence alignments. Phylogeny estimation
+ can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods,
+ and several methods handling incomplete distance matrices (NJ*,
+ BIONJ*, MVR*, and the corresponding triangle method). Some functions
+ call external applications (PhyML, Clustal, T-Coffee, Muscle, MAFFT)
+ whose results are returned into R.
diff --git a/debian/copyright b/debian/copyright
index fd1d8c7..5c150e2 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,7 +4,7 @@ Upstream-Contact: Emmanuel Paradis <Emmanuel.Paradis at ird.fr>
 Source: http://cran.r-project.org/src/contrib/
 
 Files: *
-Copyright: 2002-2016 Emmanuel Paradis, Simon Blomberg, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Gilles Didier, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Anthony Ives, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Rosemary McCloskey, Johan Nylander, Rainer Opgen-Rhein, Andrei-Alin Popescu, Manuela Royer-Carenzi, Klaus Schliep, Korbinian Strimmer, Damien de Vienne.
+Copyright: 2002-2016 Emmanuel Paradis, Simon Blomberg, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Gilles Didier, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Anthony Ives, Bradley Jones, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Rosemary McCloskey, Johan Nylander, Rainer Opgen-Rhein, Andrei-Alin Popescu, Manuela Royer-Carenzi, Klaus Schliep, Korbinian Strimmer, Damien de Vienne.
 License: GPL-2+
 
 Files: debian/*
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
index 2bb326f..aa154c9 100644
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -45,3 +45,13 @@ Reference:
     Title: "Analysis of Phylogenetics and Evolution with R"
     Year: 2006
     Type: book
+  - Author: Andrei-Alin Popescu and Katharina T. Huber and Emmanuel Paradis
+    Title: "ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R"
+    Journal: Bioinformatics
+    Volume: 28
+    Number: 11
+    Pages: 1536-1537
+    Year: 2012
+    DOI:  10.1093/bioinformatics/bts184
+    URL: http://bioinformatics.oxfordjournals.org/content/28/11/1536.full
+    eprint: http://bioinformatics.oxfordjournals.org/content/28/11/1536.full.pdf+html

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