[Blends-commit] r3444 - /projects/med/trunk/debian-med/tasks/bio-phylogeny

Mon Jun 25 13:33:27 UTC 2012

Author: tille
Date: Mon Jun 25 13:33:27 2012
New Revision: 3444

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3444
Log:
Remove extra information from packages in SVN for bio-phylogeny

Modified:
    projects/med/trunk/debian-med/tasks/bio-phylogeny

Modified: projects/med/trunk/debian-med/tasks/bio-phylogeny
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio-phylogeny?rev=3444&op=diff
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio-phylogeny (original)
+++ projects/med/trunk/debian-med/tasks/bio-phylogeny Mon Jun 25 13:33:27 2012
@@ -81,59 +81,23 @@
 
 X-End-Category: Models of nucleotide/amino acid evolution
 
+Depends: beast-mcmc
+
+Depends: tm-align
+
+Depends: mrbayes
+
+Depends: figtree
+
+Depends: populations
+
+X-Mark: Packages in Vcs - Information about these is queried from UDD as well
+
+Depends: proalign
+
+Depends: prottest
 
 Depends: treeview
-Homepage: http://jtreeview.sourceforge.net/
-Responsible: Steffen Moeller <moeller at debian.org>
-License: GPL
-WNPP: 243771
-X-Category: Visualisation
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/treeview/trunk/
-Pkg-Description: Java re-implementation of Michael Eisen's TreeView
- TreeView creates a matrix-like display of expression data, known as
- Eisen clustering. The original implementation was a Windows program
- named TreeView by Michael Eisen. This TreeView package, sometimes also
- referred to as jTreeView, was rewritten in Java under a free license,
- the original implementation also comes with the source code, but controls
- commercial distribution. And it did not run on Unix.
- .
- Java TreeView is an extensible viewer for microarray data in
- PCL or CDT format.
-
-Depends: proalign
-Homepage: http://evol-linux1.ulb.ac.be/ueg/ProAlign/
-License: GPL
-Responsible: Charles Plessy <plessy at debian.org>
-WNPP: 378290
-Pkg-Description: Probabilistic multiple alignment program
- ProAlign performs probabilistic sequence alignments using hidden Markov
- models (HMM). It includes a graphical interface (GUI) allowing to (i)
- perform alignments of nucleotide or amino-acid sequences, (ii) view the
- quality of solutions, (iii) filter the unreliable alignment regions and
- (iv) export alignments to other softwares.
- .
- ProAlign uses a progressive method, such that multiple alignment is
- created stepwise by performing pairwise alignments in the nodes of a
- guide tree. Sequences are described with vectors of character
- probabilities, and each pairwise alignment reconstructs the ancestral
- (parent) sequence by computing the probabilities of different
- characters according to an evolutionary model. It has been published in
- Bioinformatics. 2003 Aug 12;19(12):1505-13.
-
-Depends: tm-align
-
-
-
-Depends: mrbayes
-
-Depends: figtree
-
-Depends: populations
-
-X-Mark: Packages in Vcs - Information about these is queried from UDD as well
-
-Depends: beast-mcmc
-Pkg-URL: http://people.debian.org/~tille/packages/beast-mcmc-help-wanted/
 
 Depends: phylographer
 Homepage: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html
@@ -231,26 +195,6 @@
  parameter estimates, including model-averaged phylogenies. Please note
  that the DT weights are very gross
 
-Depends: prottest
-License: GPL, MIT
-Homepage: http://darwin.uvigo.es/software/prottest.html
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/prottest/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/prottest/trunk/
-Pkg-Description: Selection of best-fit models of protein evolution
- PROTTEST (ModelTest's relative) is a program for selecting the model of
- protein evolution that best fits a given set of sequences (alignment).
- This java program is based on the Phyml program (for maximum likelihood
- calculations and optimization of parameters) and uses the PAL library as
- well. Models included are empirical substitution matrices (such as WAG,
- LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam,
- MtArt, HIVb, and HIVw) that indicate relative rates of amino acid
- replacement, and specific improvements (+I:invariable sites, +G: rate
- heterogeneity among sites, +F: observed amino acid frequencies) to
- account for the evolutionary constraints impossed by conservation of
- protein structure and function. ProtTest uses the Akaike Information
- Criterion (AIC) and other statistics (AICc and BIC) to find which of the
- candidate models best fits the data at hand.
-
 Depends: forester
 
 Depends: patristic


