BETRAN LAB

Evolutionary Biology

Links

BIOINFORMATICS

Introduction to Bioinformatics

BioComputing Hypertext Coursebook
Biocomputing For Everyone !
Bioinformatics(Genomics)
Biocomputing Course Resource List
Biocomputing in a Nutshell.
The Biocomputing Glossary
Biorithms: An introduction to algorithms used in molecular biology
Building Microarray Informatics Support
ClustalW documentation
Computational Biology Course, Martin Tompa
Computational Molecular Biology Course
Course on Bioinformatics
Courses on Bioinformatics
EMBNet Biocomputing Tutorials
Functional genomics glossaries
Fundamentals of Sequence Analysis (Caltech SAF)
How to become a bioinformatics expert
Principles of Computational Biology, Steven Salzberg.
Principles of Protein Structure Using the Internet
Protein Sequence Analysis in the Genomic Era
Practical Course "Bioinformatics: Computer Methods in Molecular Biology"
VSNS BioComputing Division
VSNS BioComputing Division Multiple Alignment,Resource Page

Software Documentation

Documentation on the major sequence databases
EMBL Nucleic Acid Sequence Database Documentation
GenBank Nucleic Acid Sequence Database Documentation
SwissProt Protein Sequence Database Documentation
Sequence Database Feature Table
CORBA Servers and Services at EBI (Oib99)

Guides to the GCG package
AGRENET's Unofficial Guide to GCG Software
PDF files for the GCG Wisconsin Package
Wisconsin Package User's guide

Guides to phylogenetics
PHYLIP Phylogeny Inference Package documentation
PHYLIP Guide (EMBNet)
PAUP tutorial

Guides on similarity searching
Bioinformatics: Elementary Sequence Analysis, Brian Golding and Dick Morton
Biological Sequences and Information
BLAST help manual
BLAST tutorial
Distant homologies: motifs, patterns, profiles
Pedestrian guide to analysing sequence databases
Exploring Distant Protein Sequence Relationships
Sequence Comparison (Keith Robison)
The Sequence and Structure Searching Site
bioWidget Consortium
Computational Genefinding
GAMS: Guide to Available Mathematical Software
Genome Data Base (GDB) and Online Mendelian Inheritance in Man (OMIM)
Introduction to Perl 5 for Web Developers (eXtropia)
Introduction to XML (eXtropia)
The MathMol Hypermedia Textbook
Molecular dynamics simulations and CHARMM
Quantitative Genetics Resources
SRS TIPS
Staden Documentation Web Site
VSNS BioComputing Division Homepage
VSNS BioComputing Hypertext Coursebook - Alignment, Networking, Phylogenetics, Protein Folding etc.

Bioinformatics libraries, papers & theory Projects

Open Bioinformatics Foundation
The Bioperl Project
The Biopython Project
The BioSQL/OBDA Project

Formats
GFF: a proposed exchange format for gene-finding features

Sites and Collections
The Stony Brook Algorithm Repository

Bibliographies
Bibliography on Features, Patterns, Correlations in DNA and Protein Sequences
A Bibliography on Algorithms in Linkage Analysis
A Bibliography on computational gene recognition
A Bibliography on Using Allele-Sharing Methods in Linkage Analysis
Forsdyke's Bioinformatics background papers
Lloyd Allison - Bibliography
Publications on Molecular Evolution & Population Genetics
Publications on Physical Mapping and Genome Rearrangements
Publications on Sequence Analysis
Online papers: Protein Structure Prediction , RNA Secondary Structure Prediction, Sequence Alignment, Hidden Markov Model Comparison

Open Source, Freeware and Shareware

Operating Systems
GNU/Linux - an operating system based on the Linux kernel.

GNU/Linux Distributions
Red Hat
Debian
SuSE

Linux Documentation Project (LDP)

The *BSD Operating systems FreeBSD, OpenBSD , NetBSD . Network Services

Apache (web server)
bind (domain naming service, a critical Internet infrastructure service)
Mailman (mailing list manager)
Samba (supports interoperability with Windows clients by acting as a Windows file and print server)
Postfix (email server)
Sendmail (email server).

Relational Database Management Systems (RDBMSs)

MySQL (database emphasizing speed)
PostgreSQL (database emphasizing functionality)

Desktop applications

Evolution (email client as well as calendar and contact manager)
Mozilla (web browser and email client)
OpenOffice.org (office suite, including word processor, spreadsheet, and presentation software)
LaTeX (powerful typesetting system)
The GIMP (bitmapped image editor)
KOffice (office suite)

Development Tools/Languages

Bugzilla (Bug tracking tool)
CVS (software version management tool)
GNAT (implementation of Ada programming language)
Emacs (text editor)
GNU Compiler Collection (GCC, a suite of compilation tools for C, C++, and several other languages).
JBoss (J2EE-compliant web application server
TAO (The ACE ORB, in implementation of a CORBA ORB)
Perl (programming/scripting language)
PHP (hypertext preprocessor used for web development)
Python (another programming/scripting language)
Vim (text editor)
Tcl/Tk (scripting language and a graphical user interface toolkit)
LAMP (an abbreviation for Linux, Apache, MySQL and PHP/Perl/Python)

Web Application Development / Content Management

Zope (website development tool)
Plone (content management system)
Midgard (content management system)
OpenCMS (content management system)
Typo3 (content management system)

Graphical user interface (GUI) infrastructure

GNOME (a desktop environment)
KDE (also a desktop environment)
XFree86 (graphics infrastructure which implements the X window system)

Security

Nessus (network security scanner)
Nmap (network configuration scanner)
OpenSSH (secure replacement for telnet, rcp, and ftp)
OpenSSL (library implementing the SSL and TLS security protocols)
Snort (intrusion detection)

Research Tools

Octave (numerical computation language)
R (language for statistical computing)

HTML/XML

The WWW Consortium(W3)
XML for Molecular Biology

JAVA

Java
Java Tutorial

C/C++

Cplusplus.com
C FAQs


Institutional Links


Links