Apple computer
The best computers on this planet (Forget Microsoft!)
http://www.apple.de
http://www.apple.com


Hardware improvement
Memory suppliers (also for DOS-computers = Windows)
http://www.MemorySuppliers.com


open source licenses:

Free Software Foundation; GNU project (Richard Stallman, 1984, Copyleft):

http://www.fsf.org

 

definition open source, several licenses (Eric S. Raymond, 1998, marketing project of GNU)

http://www.opensource.org

The Cathedral and the Bazaar:

http://catb.org/~esr/writings/cathedral-bazaar/

 

software patents:

http://swpat.ffii.org/

 

open-source software for molecular biology:

lists of links:

sets of modules for molecular biology applications written in different programming languages (BioPerl, BioPython, BioJava usw.) (Linux, Windows, Mac):

http://www.open-bio.org

 

Molecular Linux:

http://bioinformatics.org/software/index.php3

 

overview on software for different platforms:

http://bioinformatics.org/softwaremap/?form_cat=2

 

packgages designed for sequence analysis (and more):

EMBOSS:

http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ (Linux)

 

GUI for EMBOSS (KDE; alternative to JEMBOSS):

http://userpage.fu-berlin.de/~sgmd/ (Linux)

 

BIRCH (wrapper for different individual programs needed for sequence analysis etc.):

http://home.cc.umanitoba.ca/~psgendb/index.html (Linux)

 

 

Staden-package:

http://www.mrc-lmb.cam.ac.uk/pubseq/ (verschiedene Plattformen)

 

GenDB (wrapper for the annotation of microbial genomes):

http://gendb.genetik.uni-bielefeld.de/ (Linux)

 

server dedicated to sequence analysis:

http://workbench.sdsc.edu/

 

open source software suitable for the analysis of microarrays:

- Michael Eisen (Windows): http://rana.lbl.gov/

- TIGR: (Windows): http://www.tigr.org/software/tm4/

- Bioconductor.(R): http://www.bioconductor.org

- BASE (Linux): http://base.thep.lu.se/

 

Cyber-T (Webserver, but also installable locally, based on R, Linux):

http://visitor.ics.uci.edu/genex/cybert/

 

list of links pointing to freeware for Windows:

http://molbiol-tools.ca/molecular_biology_freeware.htm

sequence analysis packages: DAMBE, BioEdit, GeneDoc

drawing of chemical structures: IsisDraw

pretty design of alignments: Chroma.

 

Metafile Companion (Windows):

(editing of .emf und .wmf files; test version startable thirty times; $29,00 charge for registration)

http://www.companionsoftware.com/Products/MetafileCompanion/EvalCopyDownload.html

 

phylogenetics programs (MEGA, MrBayes, ARB):

http://www.megasoftware.net (Windows)

http://morphbank.ebc.uu.se/mrbayes/ (Linux, Mac, Windows)

http://www.arb-home.de (Linux)

list of links by Joe Felsenstein: http://evolution.genetics.washington.edu/phylip/software.html

automated phylogenetics (Server):

http://www.genetics.wustl.edu/eddy/forester/

 

HOBACGEN:

(homologous bacterial genes, Webserver, data base also installable locally (Linux)):

http://pbil.univ-lyon1.fr/databases/hobacgen.html

 

alignment programs:

local alignment (DIALIGN):

http://bibiserv.techfak.uni-bielefeld.de/dialign/  (server and program (different platforms)

 

global alignment (ClustalWX):

ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/ (different platforms)

http://www.ebi.ac.uk/clustalw/ (server)

 

supposed to be better than ClustalW or X (T-Coffee):

http://www.ch.embnet.org/software/TCoffee.html (server)

http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html

(program, Linux, Mac, Windows)

 

Genolist:

(curated database of genomes of  microorganisms (13 species) with identical GUI, server)

http://genolist.pasteur.fr

 

PEDANT

(searchable database and annotation tool of all sequenced organisms (also „genomes in progress“)

http://pedant.gsf.de/

 

FFAS:

(detection of distantly related proteins, server):

http://bioinformatics.ljcrf.edu/FFAS/

 

programs for statistics:

R (open source replacement for S/S-Plus, Linux, Windows, Mac):

http://www.R-project.org/

http://www.stat.math.ethz.ch/CRAN/

 

S-Plus (commercial, nice GUI):

http://www.insightful.com/products/splus/default.asp (Windows, Linux)

 

programs for mathematical applications:

Octave (open source replacement for MATLAB; Linux, Windows) :

http://www.octave.org/

 

MATLAB (commercial):

http://www.mathworks.com/ (Windows, Mac, Linux)

 

word processing and typography:

- Latex/Tex:

http://www.dante.de (many platforms)

 

- Ktexmaker (GUI for KDE):

http://xm1.net.free.fr/linux/ (Linux)

 

- GUI’s for Latex (WYSIWYM instead of WYSIWYG):

http://www.lyx.org (many platforms)

http://www.texmacs.org/ (Linux, Windows, MacOS)

 

open source office-package (compatible to MS-Office-files):

http://www.openoffice.org/ (Windows, Linux, Mac)

 

Unix-filesystem (FHS; filesystem hierarchy standard):

http://www.pathname.com/fhs/

 

Linux-Documentation (HOWTO, books):

http://www.tldp.org