Bioinformatics Web Log



BCI Hierarchical Agglomerative Clustering Pac...
Hierarchical Agglomerative Clustering (Barnard and Downs, 1992; Downs and Willett, 1994; Barnard and Downs, 1997) involves building a hierarchical classification of compounds in a dataset by a series of binary mergers (agglomerations), initially of indivi
Cluster Analysis and Display of Genome-wide E...
Clustering Global Optimization Methods
Clustering global optimization methods can be viewed as a modified form of the standard multistart procedure, which performs a local search from several points distributed over the entire search domain. A drawback of Multistart is that when many starting
Clustering Methods
Most of the existing approaches to document clustering are based on either probabilistic methods, or distance and similarity measures (see [FBY92]). Distance-based methods such as k-means analysis, hierarchical clustering [JD88] and nearest-neighbor clust
Clustering Methods:
Sequences are clustered into subalignments by using a similarity measure [33,34,26]. The clustered subalignments are subsequently aligned to one another by employing various consensus methods that reduce each subalignment to a single consensus sequence. E



A Cross-Comparison of a Large Dataset of Genes
Alu and RAREs & TREs
Homeobox Genes DataBase ,

Phylogeny and Evolution, Alu and RAREs & TREs

BCM Human Transcript Database Home Page
The Human Transcript Database (HTD) is a curated source for information related to RNA molecules that have been sequenced. The goal of the HTD is to provide a clone-based platform that represents as many of the human transcripts that have been sequenced a
Database NCBI


EBI MSD Database System Schema
The EBI Macromolecular Structure Database is the European Project for the collection, management and distribution of data about macromolecular structures.
Entrez-PopSet - Population Specific Data
ETH: CBRG Server - SwissProt Analysis
AllAllDB: Querying the all-against-all database of SwissProt

* MassSearch: Searching SwissProt or EMBL by protein mass after digestion * NuclPepSearch: Searching SwissProt for a nucleotide sequence (Sorry! This service currently unavailable)

* PepPepSearc

Human Genome Working Draft
This page contains links to an assembly of the current draft of the human genome. The human genome is approximately 3.2 billion bases. More than 90% of the genome has been sequenced by the International Human Genome Project, and approximately 88% is inclu
MGI Home Page
MSD Home
The EBI Macromolecular Structure Database is the European Project for the collection, management and distribution of data about macromolecular structures.
OMIM Home Page -- Online Mendelian Inheritan...
Protein Information Resource Home Page - Prot...
The Protein Information Resource (PIR), in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japanese International Protein Sequence Database (JIPID) maintains the PIR-International Protein Sequence Database --- a compr
The I.M.A.G.E. Consortium
World's largest publiuc collection of genes. (There are some software tools here too)

DB Tools


Data Management Tools
Java - Oracle Corporation
Mac ODBC Guide
Papers on Developing Database Systems and Dat...




ASN.1 Summary
 ASN.1, or Abstract Syntax Notation One, is an International Standards Organization (ISO) data representation format used to achieve interoperability between platforms. NCBI uses ASN.1 for the storage and retrieval of data such as nucleotide and protein s
DDBJ/EMBL/GenBank Feature Table DefinitionDDB...
DNA Sequence Collaborator's Page
International Nucleotide Sequence Database Collaboration
Ensembl Genome Server Schema
GDB Schema Documentation
The OPM Project

Emerging Standards in Bioinformatics


The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research. We work closely with our friends and colleagues at,, and
Mother of Perl -


AppLab Homepage
CORBA-Java based Application Wrapper
Applab Homepage
A CORBA interface to the command-line driven programs

(with primary concern on biosequence analysis tools in bio-informatics) AppLab's main goal is to develop a distributed object system, which provides an easy-to-use and well-defined access to a large

Bruce Eckel's MindView, Inc. OOP Resources
CORBA Distributed Objects For Biological Databa…
Ensembl Genome Server
Ensembl is both code (software) and data. The code is predominantly Perl at the moment (but we don't expect that to last in the long term. There is alot of talk for moving to Java for new projects, probably in the Fall 2000, with CORBA coming into play fo
Functional Genomics - The Next Big Step
After years of trying to understand gene function, scientists grasp the role of only a minority of genes. With traditional tools, investigators could look at no more than a handful of genes at a time. In the wake of genome sequencing projects, however, th

JAVA and JAVAscript


Apple Developer - MRJ Software Download
Mac OS Runtime for Java (MRJ) 2.2.2 is Apple's implementation of the Java Virtual Machine (JVM), based on Sun Microsystems' Java 1.1.8 specification. MRJ provides the runtime software needed to run Java applets and applications, and the Apple Applet Runne
Cut-N-Paste JavaScript
Featuring more than 200 FREE JavaScripts you can simply paste into your HTML
Download JDesignerPro for any platform
JDesignerPro is a rapid application development and deployment system specifically designed to help you build database driven applications that run on any browser or wireless handheld device with no programming experience necessary


Java/CORBA tools
A collection of freely available tools for CORBA and Java developers, distributed with source code and documentation.
JavaBeans component architecture is the platform-neutral architecture for the Java application environment. It's the ideal choice for developing or assembling network-aware solutions for heterogeneous hardware and operating system environments--within the
Open BSA - Biomolecular Sequence Analysis
Biomolecular Sequence Analysis is the first (together with Genomic Maps) standardized and adopted technology by Life Science Research Domain Task Force (LSR) within Object Management Group (OMG). The specification is the result of a joint submission of bo
Parabon Computation, Inc. -- Internet Computation
When you're not using your computer, its power is simply being wasted. By running Pioneer™, you connect with computers worldwide to create a massive computer, capable of solving computing problems in areas such as cancer research and digital animation.
Protein Function and Metabolic Pathways
Simple Object Access Protocol (SOAP) 1.1
SOAP is a lightweight protocol for exchange of information in a decentralized, distributed environment. It is an XML based protocol that consists of three parts: an envelope that defines a framework for describing what is in a message and how to process i
The Open Lab: About The Open Lab
The Open Lab is a not-for-profit foundation established to sponsor open collaborations in research and software development in the scientific field of computational biology.  We stand firmly on our conviction that science is for the sake of science and no

XML is a resource to gather XML documentation, DTDs and tools for biology in one central location.  It overlaps in interest and in tools with the BioPerlproject, which also hosts a page about XML.  Our goal is to provide the biology community with
Mac Web Servers: Serving Up XML
Flushing out some of the lesser-known XML-related applications for the Mac.
Welcome to Extensibility
XML Development tools
Working with XML: The Java(TM)/XML Tutorial
he JavaTM XML Tutorial, is an online manual that can quickly get you up to speed writing XML code and XML-based software for end-user applications. Using step-by-step walkthroughs and lots of code examples, the Tutorial is divided into three major parts t
XML - Oracle Corporation
XML Linking Language (XLink)
This specification defines the XML Linking Language (XLink), which allows elements to be inserted into XML documents in order to create and describe links between resources. It uses XML syntax to create structures that can describe links similar to the si
XML.ORG - The XML Industry Portal
The XML.ORG Registry is a community resource for accessing the fast-growing body of XML specifications, schemas and vocabularies being developed for vertical industries and horizontal applications. It is designed to foster collaboration and enhance commun




The JESAM package is used at the EBI to build the alignments and clusters of the EuroGeneIndexes. The software is based on the ICAtools (Parsons, J.D., Brenner, S. and Bishop, M.J., (1992), Clustering cDNA Sequences, Comput. Applic. Biosci., 8, 461-466 an
SA National Bioinformatics Institute



Gene Finding


Bioinformatics, Volume 15, Issue 11, pp. 874-...
WebGene Home Page



General Info


BioABACUS Search
BioABACUS is a searchable database of abbreviations and acronyms in Biotechnology that contains terms in such categories as: Biochemistry, Cell Biology, Computers and Internet,  Diseases, Grants, Journals, Laboratories, Medicine, Molecular Biology/Genetic
Bioinform - The Global Bioinformatics News Serv…
Bioinformatics Global News Service
Bioinformatics News Service - A targeted resource for the... was created as a targeted resource for job seekers and employers who are specifically interested in the Life Sciences. Biology Job categories in our database include Agriculture, Anatomy / Physiology, Bioinformatics / Biotechnology, Botany
BioMedNet List of Conferences
Biotech: Bioinformatics
General info from the University of Texas
CAS General Subject Vocabulary Helper
Chemical Abstrcts Hyper Dictionary
CMP243 Home Page
A bioinformatics class @ UCSC



Microfluid Array Devices for Genomics and Pharmaceutical Drug Screening
Biotechnology Company Registry
DigiScents, Inc.
GCG (Genetics Computer Group)
InforMax Inc.
Orchid - A leader in genetic diversity.
SNP-IT, SNP Identification Technology



Documentation and Bioinformatics Courses
This is a collection of documentation and courses on bioinformatics topics.



Turning Their Genes Into Green
Residents of Framingham, Massachusetts, donated their private health data in the name of science 52 years ago. Should a genomics company be allowed to profit from the heart disease studies?



General Reference Listmania Results
Bioinformatics & Computational Biology Essentials  

by Cynthia Gibas, computational biologist

Bioplanet Home Page
Bioinformatics articles, jobs, links, etc.
Science Next Wave Global Home
NextWave, the weekly on-line publication devoted to scientific training and career development, provides global news, profiles of emerging careers, and advice from experts and role models drawn from your international scientific community


Google Web Directory - Science > Biology



G E N E H A C K:weblog
Genomics: Legislation and Regulation
Myhrvold: Genomics Will Rule
Starring role in Genome Project, 02-12-01
Graduate student lands starring role in the Human Genome Project. New York Times profile of Jim Kent They may as well go ahead and give Jim Kent his Ph.D. now, considering his role in a scientific achievement destined for the history books. Kent, a gradua


Intro to Bioinformatics Course Material Index
Principles of Protein Structure Using the Internet @ Birkbeck College






Google Web Directory - Science > Biology > Business
International Biotechnology Trust
The UK's first international biotechnology investment trust


International Biotechnology Trust plc (IBT) is the UK's first approved investment trust dedicated to the biotechnology sector. It offers investors the means to invest in a carefully selected and

Welcome to GenomeWeb -- New Media for the New Biology
GenomeWeb is a growing print and electronic provider of news and information on the business and technology of

genomics and bioinformatics worldwide. GenomeWeb’s customers include research enterprises in the pharmaceutical,

agriscience, biotechnology,



Jobs and Postdoctoral Opportunities


HUM-MOLGEN: Positions in Bioscience and Medicine
Way2Goal: Postdoctoral Web Sites


Links2Go: Bioinformatics
A cool links page of Bioinformatics resources
Welcome to - Biotechnology informa... is a dynamic data-driven web site containing extensive links to valuable biotech resources and up-to-date industry and corporate information. We are dedicated to provide a high quality biotech Internet information services to the biotechnology



Institutes and Research Groups


Arizona Biotechnolgy Computing Facility
Tutoring, workshops, how-to's, tools, software
Center for Computational Biology - MSU
Computational Biology at UC Santa Cruz
Department of Molecular Biotechnology
University of Washington
EBI, the European Bioinformatics Institute
The EMBL Outstation - European Bioinformatics Institute (EBI) is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.
Ensembl Genome Server
Ensembl is a joint project between EMBL-EBI and the Sanger Centre to develop a software system which produces and maintains automatic annotation on eukaryotic genomes. Human data are available now; worm and mouse will be added soon
ETH: Computational Biochemistry Research Group
Forsdyke Laboratory
Queens University, Canada. Molecular Biology and Bioinformatics - [ keywords: G0/G1 switch genes (G0S genes),  Cell Cycle,  Lymphocytes,   Immunology,  Bioinformatics, Genomics,  Theoretical Biology,  Speciation,   Evolution,  Darwin,  Romanes,  Bateson.]
Human Genome Project Research in Progress
MBL Home
Marine Biological Laboratory - Woods Hole, Mass.
Montreal Genome Centre Homepage
National Human Genome Research Institute (NHGRI)
RSBS Bioinformatics Group homepage
Australian National University
Stein Laboratory
This is a Web site run by Lincoln Stein at Cold Spring Harbor Laboratory in Cold Spring Harbor, NY. My laboratory develops software for computational biology and genome bioinformatics. Main areas of current research are pointed to by the navigation bar ab
Stockholm Bioinformatics Center
The Swiss Institute of Bioinformatics
The UCSC Center for Biomolecular Engineering
Theoretical Biophysics Group Home Page
NIH Resource for Macromolecular Modeling and Bioinformatics

Beckman Institute for Advanced Science and Technology

University of Illinois at Urbana-Champaign

UCLA Bioinformatics



Journals and Publishers


Birkhäuser Boston
Scientific and Technical Publishing in Mathematics - Physics - Biology - Biomedical Sciences - Computer Science - Engineering - Architecture
Clinical Chemistry
Genome Research
The journal focuses on genome studies in all species, and presents research that provides or aids in genome-based analyses of biological processes. The journal represents a nexus point where genomic information, applications, and technology come together
Nature Genome Information Centre
Welcome to Nature's Genome Gateway, a comprehensive web resource devoted to genomics. Access is free and the Gateway provides: * A library of original research papers, including all genome-related papers from Nature and Nature Genetics plus links to other
PROW, Protein Reviews on the Web
Protein Reviews On the Web is an online resource that features PROW Guides, authoritative short, structured reviews on proteins and protein families. The Guides provide approximately 20 standardized categories of information (abstract, biochemical functio
Scientific American
World Scientific Online Bookshop



Mass Spec




Meetings and Conferences


Bioinformatics 2001
Bioinformatics 2001 is the third major international bioinformatics meeting in Scandinavia. It is organized jointly by bioinformatics groups from the Nordic countries, and aims to cover current developments in research on all aspects of bioinformatics. B
EMO'01 Conference
First International Conference on Evolutionary, Multi-Criterion Optimization, March 7-9, 2001, Zurich, Switzerland


International Conference on Data Engineering
Linkage Disequilibrium Mapping Meeting
The conference series aims at attracting research contributions in all areas of computational molecular biology. Typical, but not exclusive, the topics of interest are genomics, molecular sequence analysis, recognition of genes and regulatory elements, mo
SAC 2001
SAC 2001 Call for Papers

16th ACM Symposium on Applied Computing

March 11-14, 2001 

Las Vegas, USA




Microarrays, Proteomics, and More Post-Genomics


Gene Expression Omnibus Home

In order to support the public use and dissemination of gene expression data, NCBI has launched the Gene Expression Omnibus. GEO is our effort to build a gene expression data repository and online resource for the retrieval of gene expression data from

genome gateway > post-genomics
The genome has been sequenced, the paper published, the champagne polished off. Now what? These pages focus on some of the developments of science in the post-genome era.

The chipping forecast: A special supplement from Nature Genetics which provides an

IPAM Function Genomics Program
Knowledge-based Analysis of Microarray Gene E...
We introduce a new method of functionally classifying genes using gene expression data from DNA microarray hybridization experiments. The method is based on the theory of support vector machines. SVMs are considered a supervised computer learning method b
Microarrays, their application and the standa...
MicroArray Informatics at the EBI: Projects ,* Expression Profiler ,a Web-based tool for microarray data analysis ,* Microarray Data Standardisation ,an international effort to adopt microarray data and annotation standards , * ArrayExpress, a public re
NHGRI Microarray Project: Home Page
papers on microarray data analysis
This is a collection of papers with emphasis on analysis of microarray (a.k.a. DNA chip) data. General reviews on microarray are occasionally included. Analysis of gene network is also occasionally included. However, papers on microarray technology itself
Peter Lee's Website at the Montreal Genome Ce...
Working with the Expression Informatics Group at the Montreal Genome Centre. We are interested in the combination of Functional Genomics and Computational Techniques in deciphering questions of genetic control. This project is a joint effort with the McGi
Research seminar on statistics of gene expres...
Scientific American: Technology and Business...
Shrinking to Enormity

DNA microarrays are reshaping basic biology--but scientists fear they may soon drown in the data

Signal Transduction Knowledge Environment
Science Mag and Stanford University Web Page with protocols, perspectives, reviews, and related info to this topic.
Silicon Genetics: gene expression software
Silicon Genetics is a leading provider of software solutions for genomic expression analysis experiments.
Software for MicroArray Gene Expression Analysis
I have tested several PC based software packages for the analysis of microarray data. All packages were demonstration versions with limited file load/save/print capability and/or a time-limited license, except ScanAlyze, Cluster and TreeView from Stanford
Statistical problems involving microarray data
U.S. Environmental Protection Agency Microarr...
forum for collaboration in the development and application of microarray technology for gene expression analysis in a number of model systems. The consortium was instigated by the Reproductive Toxicology Division (RTD) of the National Health and Environm
UCLA Bioinformatics
Web resources on Gene Expression and DNA Micr...
This site is a collection of web resources and pointers to information on large-scale gene expression studies, and especially microarray technologies. The links included are biased towards the development and applications of informatics and bioinformatics
Welcome to Speed's Microarray Homepage
What are we offering? Our hope is that we can identify simple and reliable solutions to the  statistical problems met in day to day microarray data analysis, and refer you to them.  Some of these will be our own work; much will be from others. Where possi



More Links


Bioinformatics, biocomputing: is a dynamic data-driven web site containing extensive links to valuable biotech resources and up-to-date industry and corporate information. We are dedicated to provide a high quality biotech Internet information services to the biotechnology
Links to: Tutorials and Educational Resource, Employment, Bioinformatics Servers and Home Pages, Sequence Databases and Searching, Sequence Databases, Sequence Searching, Misc Search Tools, Sequence Analysis, Analysis Tools, Alignment Tools, Sequence Fami
Computational Biology or Bioinformatics references
ETH: CBRG - Search
Molecular Biology Information Servers/BioInfo...
US Dept Commerce/NOAA/NMFS/NWFSC, Bioinformatics: Biology and Molecular Biology Resources
Molecular Evolution, Organelle Genomics & Genome Bioinformatics Resources

Univerity Montreal
Nature Net Guide
This is the first in a series of quarterly Net Guides being produced by the Nature group, each of which will sample the best of what the web has to offer in a couple of scientific disciplines, based on recommendations from Nature's staff and other experts
oligo program links
Sequence Alignment References
Tel Aviv University Bioinformatics Unit
Bioinformatics Unit, G.S. Wise Faculty of Life Sciences, Tel-Aviv University, Israel, Sites Relevant to Bioinformatics Users
The Genetic Algorithms Archive
The Genetic Algorithms Archive is a repository for information related to research in genetic algorithms and other forms of evolutionary computation. Available from this site are past issues of the GA-List digest, source code for many GA implementations,
yfleung's functional genomics home



Multiple Sequence Alignment



MSA Info


The Statistics of Sequence Similarity Scores
To assess whether a given alignment constitutes evidence for homology, it helps to know how strong an alignment can be expected from chance alone. In this context, "chance" can mean the comparison of (i) real but non-homologous sequences; (ii) real sequen








Personal Pages


Ari Kahn's Home Page: ETH
Computational Biology, Bioinformatics, BioOpera, Darwin, Phylogenetics, Physiological Ecology, Grasses, Crustaceans, Macintosh, CBRG Server
Gaston H. Gonnet personal pages
Symbolic and algebraic computation, in particular solving equations (symbolically and numerically), system development, limit and series computation and heuristic algorithms. Co-founder in 1980 of the Symbolic Computation Group at the University of Waterl
Genetics in Motion
Michael Mann - SNP, Links, Cancer
Marcel Turcotte
I study the complex relationships that exist between sequence, structure and function. Over the next five years, I intend to develop the followings three axes: 1. New models for sequence comparison. Increase in both computer processing power and amount o
Mike Hallett
Hard core phylogenetic algorithms!
Xianghong Zhou's Homepage
Research Interests: Microarray analysis / Expression profiling, Protein structure, Prediction of protein secondary structure using the singular value decomposition, The relationship between peptide sequences and their secondary structure, Protein folding





Benno Schwikowski - Research in Computational...
Our goal is to develop new methods for the reconstruction of phylogenetic trees from molecular data. An established principle for reconstructing evolution from molecular data is Parsimony. Parsimony guides the search for an explanation of the given sequen
Cladistics - Speciation Model
Comparative Evolutionary Analysis of Mitochondrial Genomes Using Maximum Likelihood

Comparative Evolutionary Analysis of Mitochondrial Genomes Using Maximum Likelihood

Comparative Evolutionary Analysis of Using Maximum Likelihood

Analysis of Mitochondrial Genomes
ETH: CBRG - Research
BioOpera, Darwin, MSAs, Phylogentics, Algorithms, publications
Introduction to Phylogeny
Molecular Phylogenetics and Evolution
MPL - Molecular Phylogenetics Lab at UC Berkeley
NEE-HOW: Databases- phylogenetics/ taxonomy
Oxford University Evolutionary Biology Group
This is a site for various projects in evolutionary biology, molecular evolution and phylogenetic epidemiology being carried out by members of the research group headed by Paul Harvey in the Department of Zoology at the University of Oxford.
Parsimony Tree Generator
Phylogenetic Analysis
Phylogenetics Resources
Phylogeny and Evolution
PPS 96' - Molecular Phylogenetics
Systematic Biology Home Page
University of Texas
Web Resources in Molecular Evolution and Systematics

Univerity of Conneticut
Western Palearctic Water Frogs + Water Frog I...





Arizona BCF: Stand-Alone Convert
Convert your "single" sequence from one format to another.
Bioinformatics Servers

BioSystems and Tools


   LabOnWeb is the first life science research engine, a collection of gene discovery tools designed to accelerate work in the lab, improve the quality and accuracy of experiments, simplify the delivery of information and help researchers make more infor
The goal of Bio-OPERA is to provide the computational biologist with a platform that takes care of all data handling and record keeping chores so that the user can concentrate on the biology aspect while the system takes care of the book keeping necessary
GeneQuiz II: a system for sequence analysis
GeneQuiz is an integrated system for large-scale biological sequence analysis, that goes from a protein sequence to a biochemical function, using a variety of search and analysis methods and up-to-date protein and DNA databases. Applying an "expert system
Provides XML powered internet and bioinformatic applications for the life sciences
PAPIA : PArallel Protein Information Analysis s…
We aim to demonstrate the power of parallel calculation technology by efficiently solving computational biology problems. For this purpose, we have developed the PAPIA (PArallel Protein Information Analysis) system.;$sessionid$MQBMOZAAAAA1PWBCHIVCFEQ?_requestid=2611 is an integrated genomics portal that provides a secure and comprehensive technology platform to simplify and accelerate life science discovery. Our research agents provide you with easy, point-and-click bioinformatics capabilities and acc


Environment for studies of molecular evolution: Powered by KL1/KLIC
ExPASy Molecular Biology Server
This is the ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB). This server is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE (Disclaimer).
Felsenstein's Phylogeny Programs
Web or e-mail servers that can analyze data for you
Logiciels pour la biologie installés sur central
Run ProtML, NucML and NJDist phylogeny programs with your data.
Molphy (Phylogenetic Analysis Package)
SeWeR: Sequence Analysis using Web Resources
What is SeWeR? SeWeR is an acronym, stands for SEquence analysis using WEb Resources. In addition to its common *dirty* use, the word SeWeR also has two meanings- first, "a medieval servant or household officer of high rank in charge of serving the dishe
SplicePredictor Online
a method to identify potential splice sites in (plant) pre-mRNA by sequence inspection


SWISS-MODEL is an Automated Protein Modelling Server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland. The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists World Wide. The
UCLA Bioinformatics Servers
The UCLA-DOE Fold Recognition Server, Verify 3D Crystal Structure Verification Server, Errat Crystal Structure Verification Server, Micro Array Database Server, RNA Editing Websitte, Uridine Insertion/Deletion Home, Uridine Insertion/Deletion Database






ftp Servers


Indiana U ftp server
This is a user-supported archive for biology software and data
Sanger UK ftp server





Biology Software for Windows NT
DNASIS software
DNA / RNA Analysis and Protein Analysis Package

• Custom plasmid map drawing

• Circular and linear restriction maps

• Customized enzyme tablets and selection criteria

• Primer design

• RNA folding

• ORF analysis

• Contig manager (automatic and manual frag

EMBOSS Homepage
EMBOSS is a new, free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval o
Darwin v. 2.0 , an interpreted computer language especially tailored to researchers in the biosciences. The system is a general tool applicable to a wide range of problems. This second release improves Darwin version 1.6 in several ways: it now contains (
Freely distributable documents and computer p...
GCG Products and Services
Data Management and Sequence Analysis

SeqStore (relational, Oracle based)

Sequence Analysis

GCG Wisconsin Package (UNIX)

MacVector (Macintosh)

OMIGA (Windows 95/98/NT systems)

Interfaces to the GCG Wisconsin Package

SeqWeb (web intranet)

SeqLab (X Window
Free Software in Molecular Biology for Macintosh and MS Windows computers


IBM techexplorer Hypermedia Browser
  IBM techexplorer is a plug-in for Navigator and Internet Explorer and an ActiveX control for applications like Microsoft PowerPoint and Word. techexplorer enables the display of TeX, LaTeX and MathML documents and the publishing of interactive scientifi
Linux Bioinformatics Software
The BioOpera Homepage
BioOpera is a joint project between the Information and Communication Systems and the Computational Biochemistry Research Group (CBRG) at the Swiss Federal Institute of Technology in Zurich. Our goal is to improve and automatize large scale analysis of ge
Unix Bioinformatics Software
Waterloo Maple: Home



Phylogenetics Software


Debian GNU/Linux -- fastdnaml
fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML (part of his PHYLIP package). Users should consult the documentation for DNAML before using this program. fastDNAml is an attempt to solve the same problem as DNAML, but to do so f
ISMLIB Other Software
MOLPHY/ProtML - uses Maximum Likelihood with protiens
LAMARC - estimating population parameters
a package of programs for computing population parameters, such as population size, population growth rate and migration rates by using likelihoods for samples of data (sequences, microsatellites, and electrophoretic polymorphisms) from populations. It ap
PAUP* 4.0
PHYLIP Home Page
PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables. These Web pages, being constructed by Joe Felsenstein of the Department of Genetics at t
Phylogenetic Analysis by Maximum Likelihood (...
Phylogeny Programs
Here are some 175 of the phylogeny packages, and 17 free servers, that I know about. Some of them are available over Felsenstein's Phylogeny Program List: Internet from ftp server machines, or by World Wide Web. The programs listed below include both fre
PROTML: Maximum Likelihood Inference of Prote...
T-REX (Tree Reconstruction)
TrExML Information
TrExML is a program derived from Olsen et al.'s fastDNAml. Whereas fastDNAml was written to be a fast program for inferring phylogenetic relationships and comparing evolutionary hypotheses, TrExML is written to provide a more exhaustive coverage of evolut



Scientific Computing




Sequence Analysis Software




Viewing Software


VMD - Visual Molecular Dynamics
NIH Resource for Macromolecular Modeling and Bioinformatics

Beckman Institute for Advanced Science and Technology

University of Illinois at Urbana-Champaign











Algorithms in Molecular Biology, Fall 1998-99
Tel Aviv University Department of Computer Science, Ron Shamir


Applixware Presentation
First International Bioinformatics Summer School 1999 (IBSS'99)

Presentation Slides

Overview, Classical Clustering Methods, Classical clustering, an example, Mixture Models based Applications, The Mixture Models Classification Approach, BClass Scheme, MCM

Biocomputing Course Resource List : Course Syllabi
Biocomputing Course Resource List : Course Syllabi
Bioinformatics at Queens University, Canada
Bioinformatics: Online Courses
The development of bioinformatics courses is still in its infancy. Only a few universities around the world offer courses specifically designed for this field. Following are the few online courses in bioinformatics currently accessible, two of which repre
This course focuses on the application of  computer science

techniques to problems arising in biology and biochemistry.  We will present mathematical models of evolution, discussions about the role bioinformatics will play in the future of drug design,

Computational Molecular Biology
This course is designed for molecular biologists and computer scientists desiring a practical, hands on approach to the field of computational molecular biology. The course is recommended for those wanting to understand the major issues concerning represe
Computer Intensive Methods in Phylogeny
Computer Intensive Methods in Phylogeny
Stanford, Susan Holmes, Copyright 1998
DEA-SIB: Module 6
Principles of Protein Structure, Comparative Protein Modelling and Visualisation
ETH: Introduction to Bioinformatics
The intention of this course is to provide biochemists with a practical guide to bioinformatics.  This will be achieved by examining various software tools currently available to the community.  Our focus will lie both on how one uses these tools and on
Introduction to the Bootstrap:Statistics 208
Stanford, Susan Holmes, Copyright 1998
IRBM practical course
Frontiers of Protein Structure Prediction 1995.


Links2Go: Bioinformatics: Academic/Degree Programs
Not Found
Bioinformatics and Computational Biology at George Mason University


Scientists complete genetic milestone
Mapping DNA for Newbies from MSNBC