WEB sPACE GENOMICS

jdna02.gif (12648 bytes) WEB sPACE GENOMICS

VFU Brno PARU Ceske Budejovice	Alignments
Glossary of terms !!! The glossary from the Fundamentals of Molecular Evolution (Li and Grauer 1991) "Dictionary of terms (czech - Flegr)	ParuFVL-CZ ParuCAS-CZ (Jula a Mira)
Any recommendations and suggestions E-mail me ----------»»»

This site is basically for my personal use, as I'm being involved with rDNA the site is biased so. Sorry of inconvenience. I may improve it in the near future.

The process of building a tree is becoming routine with the use of growing number of sequences, software and faster and faster PCs/Macs. At this point I have to mention that I use PSs, just because (would like to try to work out some of the analysis on Mac) and additionally I use only the programs that work on DOS/Windows systems (there is a near future and I get a new PS and I install Linux).

Molecular Systematics and Evolution of Microorganisms
Index: http://www.may.ie/academic/biology/james/toc.html

NCBI

TreeBASE
Its main function is to store published phylogenetic trees and data matrices. It also includes bibliographic information on phylogenetic studies, and some details on taxa, characters, algorithms used, and analyses performed.

Workshop on Molecular Evolution 2000
lectures (PDF) included

THE WEB OF SCIENCE

Education at MBL Woods Hole - 2001 courses

Programs:

How fast is my new computer? (by Ziheng Yang)

All you are probably looking for is listed on Joe Felselnstein Phylogenetic programs page!!!!

PAML http://abacus.gene.ucl.ac.uk/software/paml.html (PDF manual) by Ziheng Yang
PAUP*
MEGA2 (files from Nei and Kumur 2000 Molecular Evolution and Phylogenetics 2000)
COMPONENT
BioEdit
Clustal X
DSCE
ForCon
NEXUS Data Editor
TreeView
MUST
Slow-Fast
Tree-Puzzle

Books:

E-mails/URLs:

Herve Philippe - [email protected] http://sorex.snv.jussieu.fr/ (MUST2000, Slow-Fast)
John R. Barta - [email protected]
John T. Ellis - [email protected] http://www.science.uts.edu.au/cmb/mpu/
Alan M. Johnson - [email protected] http://www.science.uts.edu.au/cmb/mpu/
Jim Wilgenbusch / Dave Swofford - [email protected] http://www.lms.si.edu/PAUP/ (PAUP*4)
Jan Keithly - [email protected] http://www.wadsworth.org/resnres/bios/keithly.htm
Rod Page - [email protected] http://taxonomy.zoology.gla.ac.uk/rod/rod.html (TreeView, COMPONENT, NDE.....)
Joe Felsenstein - [email protected] depts.washington.edu/genetics/faculty/felsenstein.html (PHILIP)
John P. Huelsenbeck - [email protected] brahms.biology.rochester.edu (CodonBootstrap, MrBayes) **
Ziheng Yang - [email protected] http://abacus.gene.ucl.ac.uk/ziheng/ziheng.html (PAML) **
**see links inside

Journals:

American Journal of Human Genetics
American Naturalists
Biometrics
Computer Application in BioSciences (CABIOS)
Evolution
Genetics
Journal of Molecular Evolution
Journal of Mathematical Biology
Molecular Biology and Evolution
Nature
Proceedings of National Academy of Sciences of USA
Science
Systematic Biology
Trends in Ecology and Evolution

Start with retrieving the sequences

NCBI

ENTREZ - GENBANK

GSDB: Accession number query

DDJB

Aligning the sequences

DDJB - Database Searches and Data Analyses.

PAIRWISE SEQUENCE ALIGNMENT

Blast 2 Sequences (NCBI)

MULTIPLE SEQUENCE ALIGNMENT

BCM: Multiple Sequence Alignments

Default parameters.

CLUSTALW at DDBJ (Japan)

Change some parameters

CLUSTALW at PBIL Lyon (France)

Change parameters as you like

Work it on your computer !!!

CLUSTALX (Download)

Do what ever you want (PS-Windows).

On line course of ClustalX (tutorial)

Converting different formats (from-to)

ForCON (Download)

Secondary structure

DCSE

Ribosomal Database Project II

The rRNA WWW Server

EDITING (MANUAL) ALIGNMENT

Work it on your computer !!!

SeeView (Download)

BioEdit (Download)

Producing the tree

PAUP*

You have to bay this software!!! But anyway it it worth the money, especially must be on Mac.

PAUP* Lits of Commands and Description

All commands listed.... find your command!!!

PAUP* Tutorial

First essential steps of PAUP*

PAUP* Documentation

Some more of documentation....

Interpretation of the trees and methods used in variety of scientific papers

I hope to enlarge this part. Recently (last 2-3) years there is "too much" of the phylogenetic analysis in variety of papers, and probably there is not enough people to review all that, so sometimes the tree is not the tree you would "produce" yourself with the data retrieved from the databases.

Methods develop, computers run faster....

Try to reanalyze all the trees, I try but it takes time, but it is worth the effort you learn a lot anyway.

Do not miss these WWW links!!!

Rod Page - web site

http://lyco.lycoming.edu/~newman/rrna/16Salign.htm

Genome Sequenceing Centers

Molecular systematics and Evolution of Microorganisms (1999)

http://www.cse.ucsc.edu/research/compbio/ssurrna.html

Parasite Genome Internet Resources and Contacts

Phylogeny Programs

http://www.bbsrc.ac.uk/biolist.html

Parasite Genom (EMBL)