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/ _______________________________________________ Blends-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/blends-commit
