[Blends-commit] r2199 - projects/med/trunk/debian-med/tasks
Debian Pure Blends Subversion Commit
noreply at alioth.debian.org
Wed Jun 9 09:50:14 UTC 2010
Author: moeller
Date: Wed Jun 9 09:50:13 2010
New Revision: 2199
URL: http://svn.debian.org/viewsvn/blends?rev=2199&view=rev
Log:
Cleaned up wording for biolinux distribution.
Modified:
projects/med/trunk/debian-med/tasks/bio
Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/viewsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2199&view=diff&r1=2199&r2=2198&p1=projects/med/trunk/debian-med/tasks/bio&p2=projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Wed Jun 9 09:50:13 2010
@@ -1830,8 +1830,7 @@
available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK
database entries or sequence in FASTA or raw format. Extra sequence features
can be in EMBL, GENBANK or GFF format.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: act
Homepage: http://www.sanger.ac.uk/Software/ACT/
@@ -1852,8 +1851,7 @@
.
To see ACT in action go to the examples page
http://www.sanger.ac.uk/Software/ACT/Examples/
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: acedb-other-dotter, acedb-other-belvu
@@ -2092,8 +2090,7 @@
APE aims to be both a computing tool to analyse phylogenetic and
evolutionary data, and an environment to develop and implement new
analytical methods.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: caftools
Homepage: http://www.sanger.ac.uk/Software/formats/CAF/userguide.shtml
@@ -2155,8 +2152,7 @@
This script will chop up a large sequence, run blast on each bit and
then write out an EMBL feature table and a MSPcrunch -d file
containing the hits.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: blixem
Homepage: http://bioinformatics.abc.hu/tothg/biocomp/other/Blixem.html
@@ -2168,8 +2164,7 @@
is an interactive browser of pairwise Blast matches that have been
stacked up in a ma ster-slave multiple alignment
Remark: The link to the source archive on the web pages is not valid any more - it might be a problem to obtain the source.
- This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: cap3
Homepage: http://genome.cs.mtu.edu/cap/cap3.html
@@ -2224,8 +2219,7 @@
With recent developments, cd-hit package offers new programs for DNA
sequence clustering and comparing two databases. It also has lots of
new options for clustering control.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Comment: BioLinux contains a clcworkbench package which is available
at http://www.clcbio.com/index.php?id=28 but this seems to be only
@@ -2281,10 +2275,9 @@
Dotter provides a tool to explore the visual appearance of this
landscape, as well as a tool to examine the sequence alignment it
represents.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
.
- Homepage is currently unavailable but the source might be
+ The package's homepage is currently unavailable but the source might be
obtainable from freebsd.org.
Depends: dotur
@@ -2301,8 +2294,7 @@
using the distance matrix. Using the OTU composition data, dotur
constructs collector's and rarefaction curves for sampling intensity,
richness estimators, and diversity indices.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: estferret
Homepage: http://legr.liv.ac.uk/EST-ferret/index.htm
@@ -2349,8 +2341,7 @@
of flat file formats, sources of which can be serve as inputs for
some gene annotation and gene expression profiling tools, and also as
a MySQL database or web-browsable search tool.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: estscan
Homepage: http://estscan.sourceforge.net/
@@ -2383,8 +2374,7 @@
* Iseli C, Jongeneel CV, Bucher P. (1999) ESTScan: a program for
detecting, evaluating, and reconstructing potential coding regions in
EST sequences. Proc Int Conf Intell Syst Mol Biol.138-48.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: fasta
Homepage: http://www.ebi.ac.uk/Tools/fasta/
@@ -2405,8 +2395,7 @@
decreases the number of background hits. Not every word hit is
investigated but instead initially looks for segment's containing
several nearby hits.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: fluctuate
Homepage: http://evolution.gs.washington.edu/lamarc/fluctuate.html
@@ -2439,8 +2428,7 @@
analyses. Currently, it includes the phylogenetic tree visualization
and manipulation tool ATV and implementations of the SDI algorithm
and the RIO method (http://www.phylosoft.org/).
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: jalview
Homepage: http://www.jalview.org/
@@ -2469,8 +2457,7 @@
programs Coalesce, Fluctuate, and Recombine, which are no longer
being supported. The programs are memory-intensive but can run
effectively on workstations.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: lucy
Homepage: http://rcc.uga.edu/applications/bioinformatics/lucy.html
@@ -2496,8 +2483,7 @@
“next-generation” sequencers.
.
See also the SourceForge page at http://lucy.sourceforge.net/.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: maxd
Homepage: http://www.bioinf.man.ac.uk/microarray/maxd/
@@ -2515,8 +2501,7 @@
maxdView - modular and easily extensible data visualisation and
analysis environment
maxdSetup - installation management utility
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: mesquite
Homepage: http://mesquiteproject.org/mesquite/mesquite.html
@@ -2543,8 +2528,7 @@
There is a brief outline of features, which includes
screenshots. Mesquite is not primarily designed to infer phylogenetic
trees, but rather for diverse analyses using already inferred trees.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: migrate
Homepage: http://popgen.scs.fsu.edu/Migrate-n.html
@@ -2566,8 +2550,7 @@
mutation rate among loci. Profile likelihood tables, Percentiles,
Likelihood-ratio tests, and simple plots of the log-likelihood
surfaces for all populations and all loci.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: mrbayes
Homepage: http://mrbayes.csit.fsu.edu/
@@ -2589,8 +2572,7 @@
format. The output is several files with the parameters that were
sampled by the MCMC algorithm. MrBayes can summarize the information
in these files for the user. The program features include:
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: msatfinder
Homepage: http://www.genomics.ceh.ac.uk/msatfinder/
@@ -2605,8 +2587,7 @@
protein sequences (as long as the maximum size of all sequences does
not exceed 10MB). Nucleotide and amino acid sequences in GenBank,
FASTA, EMBL and Swissprot formats are supported.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: mview
Homepage: http://bio-mview.sourceforge.net/
@@ -2622,8 +2603,7 @@
multiple alignment adding optional HTML markup to control colouring
and web page layout. MView is not a multiple alignment program, nor
is it a general purpose alignment editor.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: oligoarrayaux
Homepage: http://dinamelt.bioinfo.rpi.edu/OligoArrayAux.php
@@ -2644,7 +2624,7 @@
http://dinamelt.bioinfo.rpi.edu/download.php and you should probably
read http://dinamelt.bioinfo.rpi.edu/ if you want to know more about
"Prediction of Melting Profiles for Nucleic Acids".
-Remark: This package is included into BioLinux distribution
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Finally it is hard to find some documentation what OligoArrayAux is
really doing because it is only specified into relation to OligoArray
(as precondition) and UNAFold (as subset of this) but BioLinux
@@ -2670,8 +2650,7 @@
Estimating diversifying selection and functional constraint in the
presence of recombination.
Genetics doi:10.1534/genetics.105.044917.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: paml
Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html
@@ -2687,8 +2666,7 @@
be used to estimate parameters and test hypotheses to study the
evolutionary process, when you have reconstructed trees using other
programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: partigene
Homepage: http://www.nematodes.org/bioinformatics/PartiGene/
@@ -2702,8 +2680,7 @@
multi-step software tool which takes sequences (usually ESTs) and
creates a dataabase of a non-redundant set of sequence objects
(putative genes) which we term a partial genome.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: pfaat
Homepage: http://pfaat.sourceforge.net/
@@ -2715,8 +2692,7 @@
annotate multiple sequence alignments. The annotation features are a
key component as they provide a framework to for further sequence,
structure and statistical analysis.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: pftools
Homepage: http://www.isrec.isb-sib.ch/profile/profile.html
@@ -2727,8 +2703,7 @@
The 'pftools' package is a collection of experimental programs
supporting the generalized profile format and search method of
PROSITE.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: prank
Homepage: http://www.ebi.ac.uk/goldman-srv/prank/
@@ -2762,8 +2737,7 @@
may go wrong and how to avoid that, read this explanation of
differences between PRANK and traditional progressive alignment
methods.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Comment: priam
BioLinux contains a priam package which is available at
@@ -2781,8 +2755,7 @@
and translates them optimally to produce putative peptides. prot4EST
intergrates a number of programs to overcome problems inherent with
translating ESTs.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: qtlcart
Homepage: http://statgen.ncsu.edu/qtlcart/
@@ -2795,8 +2768,7 @@
will aid in locating the genes that control quantitative traits using
a molecular map of markers. It includes some programs to allow
simulation studies of experiments.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: rbs-finder
Homepage: http://www.genomics.jhu.edu/RBSfinder/
@@ -2813,8 +2785,7 @@
.
You can find more detailed information at
http://nbc11.biologie.uni-kl.de/docbook/doc_userguide_bioinformatics_server/chunk/ch01s06.html
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: recombine
Homepage: http://evolution.genetics.washington.edu/lamarc/recombine.html
@@ -2867,8 +2838,7 @@
downloadable source code without any license or copyright statement -
so it has to be clarified whether we are able to distribute this code
or not.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: taverna
@@ -2894,8 +2864,7 @@
workflows. The Taverna workbench, myExperiment and associated
components are developed and maintained by the myGrid team, in
collaboration with the open source community.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: taxinspector
Homepage: http://nebc.nox.ac.uk/projects/taxinspector.html
@@ -2906,8 +2875,7 @@
TaxInspector is a browser for entries in the NCBI taxonomy. It is
designed to run as a plugin to annotation software such as maxdLoad2
and Pedro, but also has a standalone mode.
-Remark: This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: tetra
Homepage: http://www.megx.net/tetra/
@@ -2925,9 +2893,7 @@
TETRA. At the time writing, no decisions have been made about
adapting and cross-compiling the Mac OS X code for this platform. A
Linux version might happen when REALbasic's Linux IDE is more mature.
- .
- This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: trace2dbest
Homepage: http://www.nematodes.org/bioinformatics/trace2dbEST/
@@ -2950,9 +2916,7 @@
use of other software (available free under academic licence) that
you will need to have installed, namely phred, cross_match and
(optionaly) BLAST.
- .
- This package is included into BioLinux distribution
- http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Depends: profit
Homepage: http://www.bioinf.org.uk/software/profit/
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