Jan Slapeta WEB sPACE GENOMICS

                                         (old version)

alias Slapeta's HomePage and some links, help and maybe advice or what ever I add.
I am updating/rewriting the page almost every day but still many parts are unpolished and untidy
 
Google www.google.com 
NCBI (GenBank) http://www.ncbi.nlm.nih.gov/
ISI WoS http://isi4.isiknowledge.com/ 
BiblioVIE http://bibliovie.inist.fr/revues_chercher.php 
 		 My home-page:
http://www.geocities.com/slapeta/ (US - mirror)
http://www.mujweb.cz/www/iroger/genomics/  (CZ-home)
http://www.mujweb.cz/www/iroger/

http://mail.yahoo.com/ 
http://webmail.tele2internet.fr/  
http://mailhost.pop.u-psud.fr/

OligoCalculator

http://foo.maths.uq.edu.au/~huber/bellerophon.pl
http://rdp.cme.msu.edu/cgis/chimera.cgi?su=SSU

http://pubcrawler.gen.tcd.ie/db/slapeta/

Gregarine server http://science.peru.edu/gregarina/index.html

07/04/2004

I am now trying to rebuild this page, and make it more useful than it used to be, at least for me!!! 

My CV etc.
Contact me?
links
links to people
Journals www
PAUP*- help line that might turn useful (under reconstruction, I probably will never finish that I wanted to in late 2001, but too many thinks had a priority)

CryptosporidiumTAXID (still under construction)

Phylogenetics - books to be recommended
Bioinformatics / JAVA / Perl - books I try to learn

Upcoming conferences of my interest:

 

 

 

MyNedstat URL: http://www.mynedstat.com
 
Phylogenetics - books to be recommended (linked to www.amazon.com etc.)

Page (11172 bytes) MEGA..jpg (35885 bytes) Grauer (4946 bytes) Avise (4404 bytes) Wheeler (2753 bytes) Schuh (2426 bytes)

  • The first 3 above books are excellent reviews of a subject, the second is direct reference to MEGA2 program, and Graur and Li is just standart itself, too. The next three are suplement and for those interested in how phylogenetics may turn into plylogeography or to change our view on systematics and species concept. 
  • Hall Barry G.(2001) Phylogenetic Trees Made Easy: A How-To Manual for Molecular Biologists (very useful for all beginners - step-by-step tutorial see reviews in Science and Nature (by Van de Peer and Mayer) Sinauer
  • David M. Hillis, Craig Moritz, Barbara K. Mable (1996) Molecular Systematics, Second Edition. (may seem outdated by the date, but this is a real The Book!!! - get it if you mean it serious with setting and running a systematic experiment based on molecular methods in any field of life on Earth) Sinauer
  • Felsenstein Joe (2003) Inferring Phylogenies Sinauer (This is the book by the inventor of several phylogenetic methods and the autor of PHYLIP, this book should be included in the library of anyone who has anythink to do with phylogeny and methods included in PHYLIP)
  • Marco Salemi, Anne-Mieke Vandamme, Eds. (2003) The Phylogenetic Handbook Cambridge University Press (This book is a excellent review of methods as well as hands on training by authors of the phylogenetic tools - "how to use my program" so if you wonder about a method and the use of a particular program this book is for you, and for me too :-); more importantly a chapter about alignment is included and the use of Clustal et al.) book homepage, Amazon

 

... few more exist I will add them soon or later

Major phylogenetic programs I regularly use; links and downloads/updates (check frequently):

MrBayes - http://morphbank.ebc.uu.se/mrbayes/ 
PAUP* - http://paup.csit.fsu.edu/about.html 
PHYLIP - http://evolution.genetics.washington.edu/phylip.html 
PAML - http://abacus.gene.ucl.ac.uk/software/paml.html 
MOLPHY (ProtML) http://www.ism.ac.jp/software/ismlib/softother.e.html 

Some more (recently attantion)

PHYML http://www.lirmm.fr/~guindon/phyml.html (fast ML)
GAME http://www.lirmm.fr/~guindon/gamma.html (estimates gamma, fast)

Bioinformatics / JAVA / Perl - books I try to learn

The following books I got and found them useful or okey....

  • Tisdall JD (2001) Beginning Perl for Bioinformatics. amazon.com, O' Reilly Online Catalog
  • Greg Gibson and Spencer Muse (2001). A Primer of Genome Science. Sinauer 
  • Mary Campione, Kathy Walrath, Alison Huml (2001) The Java(TM) Tutorial: A Short Course on the Basics (3rd Edition) Amazon, SUN books
  • Joao Carlos Setubal, Joao Meidanis (1997). Introduction to Computational Molecular Biology amazon.com
  • Mount DW (2001). Bioinformatics: Sequence and Genome Analysis Amazon

Have not seen yet....but will...

  • Durbin et al. (1999). Biological Sequence Analysis : Probabilistic Models of Proteins and Nucleic Acids Amazon
  • Pierre Baldi and Søren Brunak (2001). Bioinformatics: The Machine Learning Approach, Second Edition MIT-press

Addresses to people etc.

see links inside

PARASITE genoms

 

 Picoeukaryotes (with attention to Alveolata)

  • NCBI link to Alveolata: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=33630 
  • PICODIV a European FP5 program http://www.sb-roscoff.fr/Phyto/PICODIV/ 
    see: 
    Moreira D, Lopez-Garcia P. (2002) The molecular ecology of microbial eukaryotes unveils a hidden world. Trends Microbiol 10(1):31-8. [Link]
    Vaulot D., Romari K., Not F. (2002) Are autotrophs less diverse than heterotrophs in marine picoplankton? Trends Microbiol 10(6):266-7. [Link]
    Edgcomb VP, Kysela DT, Teske A, de Vera Gomez A, Sogin ML. (2002) Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. Proc Natl Acad Sci USA 99(11):7658-62 [Link]
    Lopez-Garcia P, Philippe H, Gail F, Moreira D. (2003) Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge. Proc Natl Acad Sci USA 100(2):697-702 [Link]
     
    NASA Astrabiology Institute http://nai.arc.nasa.gov/index.cfm 
    Astrobiology Magazine http://www.astrobio.net/ 

 Protein folding / helices etc.

 Sorted links / www / ftp
  LIGHT CYCLE / real-time PCR

RECENT FAVORITES

  • http://cleanup.stevengould.org/ - CleanUp!!! cleans and helps your Win/PC system to run, FREEEE....

  • The Open Bioinformatics Foundation  http://www.open-bio.org/ (BioPerl, BioJava, BioPython....)

  • bioinformatics.org https://bioinformatics.org/ - tons of links and forums ..... (free registration)
  • Welcome to the Workshop on Molecular Evolution (Woods Hole, MA) http://newfish.mbl.edu/Course/ = there is basicaly everythink you want to know and are afraid to ask, most of the lectures have pdf or ppt version, there are most of the programs for molecular evolution listed with tutorials, manuals online courses etc. This early course is probably the best in the mol. evolution. So, if you have problems with some mol. phylogenetic issue try here ! IT IS WORTH IT!!!

Journals

 

  • I must add several those I now work more with.....

 

  

 
 

Home institute (French Research Council - CNRS):

UMR-CNRS 8079 "Ecologie, Systématique & Evolution"
Université Paris-Sud, bâtiment 360
91405 ORSAY Cedex, France  - www.igmors.u-psud.fr 

Former institutes:
Department of Health - State of New York, Albany in the lab of Dr. Janet S. Keithly
Department of Parasitology, Faculty of Veterinary  Medicine, University of Veterinary and Pharmaceutical Sciences Brno www.vfu.cz 
Laboratory of Molecular Parasitology - Institute of Parasitology Academy of Sciences of the Czech Republic 
 

Want to contact me?

official/work e-mail: [email protected] 

e-mail (forever - hopefully!!!): [email protected]
 

 

 

Hosted by www.Geocities.ws

1