[Cdd-commits] r294 - in projects/med/trunk: . menu menu/bio menu/docs

[Andreas Tille]

Author: tille
Date: Fri Sep 17 00:09:44 2004
New Revision: 294

Added:
   projects/med/trunk/menu/bio/molphy.txt
   projects/med/trunk/menu/bio/phylip.txt
Removed:
   projects/med/trunk/menu/dent
   projects/med/trunk/menu/docs/
   projects/med/trunk/menu/imaging
   projects/med/trunk/menu/pharmacy
   projects/med/trunk/menu/physics
   projects/med/trunk/menu/tools
Modified:
   projects/med/trunk/VERSION
   projects/med/trunk/menu/bio/ncbi-tools-bin.menu
Log:
Merged changes for version 0.8.9 into svn archive


Modified: projects/med/trunk/VERSION
==============================================================================
--- projects/med/trunk/VERSION	(original)
+++ projects/med/trunk/VERSION	Fri Sep 17 00:09:44 2004
@@ -1 +1 @@
-0.8.4
+0.8.9

Added: projects/med/trunk/menu/bio/molphy.txt
==============================================================================
--- (empty file)
+++ projects/med/trunk/menu/bio/molphy.txt	Fri Sep 17 00:09:44 2004
@@ -0,0 +1,17 @@
+Some information about MolPhy from the Debian-Med project.
+
+Molphy is an extensive set of tools for MOLecular PHYlogenetics.  You can
+get a first overview by the two manpages
+
+   man protml
+   man mollist
+
+For further reading the files in 
+
+   /usr/share/doc/molphy
+
+are suggested.  Moreover you can find several examples in
+
+   /usr/share/doc/molphy/examples/tests/
+
+which contains a makefile to give you an idea how to call the MolPhy tools.

Modified: projects/med/trunk/menu/bio/ncbi-tools-bin.menu
==============================================================================
--- projects/med/trunk/menu/bio/ncbi-tools-bin.menu	(original)
+++ projects/med/trunk/menu/bio/ncbi-tools-bin.menu	Fri Sep 17 00:09:44 2004
@@ -1,3 +1,4 @@
+# The lot of entries just blast the menu to much
 ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asn2asn" needs="X11" \
 	section="Med/Biology/ncbi-tools-bin" title="asn2asn" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
 ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asn2ff" needs="X11" \

Added: projects/med/trunk/menu/bio/phylip.txt
==============================================================================
--- (empty file)
+++ projects/med/trunk/menu/bio/phylip.txt	Fri Sep 17 00:09:44 2004
@@ -0,0 +1,26 @@
+Some information about Phylip from the Debian-Med project.
+
+  A package of programs for inferring phylogenies.
+
+  The PHYLogeny Inference Package is a package of programs for inferring
+  phylogenies (evolutionary trees) from sequences.
+  Methods that are available in the package include parsimony, distance
+  matrix, and likelihood methods, including bootstrapping and consensus
+  trees. Data types that can be handled include molecular sequences, gene
+  frequencies, restriction sites, distance matrices, and 0/1 discrete
+  characters.
+
+If you call phylip in a text console you get some help:
+
+ Usage: /usr/bin/phylip <program>
+   Existing programs are:
+ clique	  dnacomp   dnamlk    dollop	drawtree  kitsch    penny     retree
+ consense  dnadist   dnamove   dolmove	factor	  mix	    protdist  seqboot
+ contml	  dnainvar  dnapars   dolpenny	fitch	  move	    protpars
+ contrast  dnaml     dnapenny  drawgram	gendist   neighbor  restml
+
+which is quite the same information as the Debian manpage of phylip
+contains.
+There is extensive documentation at /usr/share/doc/phylip and some
+examples in the examples dir at this location.
+            
\ No newline at end of file