OEGE online tools
- Hardy-Weinberg equilibrium calculator – chi-sq Hardy-Weinberg equilibrium test calculator for biallelic markers.
- Sequence tools – basic tools for DNA sequence manipulation – reverse complement, GC content etc.
- CubeX – online web tool for calculation of pairwise linkage disequilibrium using exact solution.
Programs available at this site
- MIDAS – interallelic linkage disequilibrium analysis for multiallelic and biallelic markers with interactive graphical interface.
- CubeX – see description above. You can also download a version for batch use with large datasets from the CubeX page.
Software links
(alphabetical order)
- Biocompute applications website – a variety of genetics programs http://apps.biocompute.org.uk
- An alphabetic list of genetic analysis software – http://linkage.rockefeller.edu/soft/list1.html
- Biological software – http://bioweb.pasteur.fr/intro-uk.html
- Free statistical software – http://users.aol.com/johnp71/javasta2.html
- Phylogeny software – http://evolution.genetics.washington.edu/phylip/software.html
- Statistical software components – http://econpapers.repec.org/software/bocbocode/
- Linkage Disequilibrium analysis software
Pedigree and Epidemiological data management
- Personal Ancestral File (PAF) – freely downloadable pedigree filing software: “PAF was developed by the LDS Church and is extensively used by genealogists for filing family and ancestral information. It exports and imports standard GED format which is compatible with various clinical and genealogical programs. It is very valuable for information keeping where extended tracing of families is being undertaken and is therefore widely used by private individuals interested in their own families as well as having utility for genetics researchers undertaking similar tasks.” – http://www.familysearch.org/eng/paf/
Bioinformatics links
(alphabetical order)
- Bioinformatics links: “links to informatics resources on the net” – http://www.bioplanet.com/bioinformatics_links.htm
- Bioinformatics links directory: “The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. All of the resources are free or available for a nominal fee. The links listed in this directory are selected on the basis of recommendations from bioinformatics experts in the field. We make every effort to list useful, well tested resources instead listing all tools.” – http://bioinformatics.ubc.ca/resources/links_directory/
- Bioinformatics references and links: “provides recent literature overview of Bioinformatics and related topics” – http://lansbury.bwh.harvard.edu/bioinformatics.htm
- Bioinformatics World: “A collection of evaluated bioinformatics programs and databases created by Herbert Mayer” – http://homepage.univie.ac.at/herbert.mayer/
Statistical links
(alphabetical order)
- BMJ – statistical notes (+many clinical reviews and ABCs) led by Bland and Altman: “Standard deviations and standard errors. Treatment allocation by minimisation. Diagnostic tests 4: likelihood ratios. The logrank test. Interaction revisited: the difference between two estimates. Validating scales and indexes. Analysing controlled trials with baseline and follow up measurements. Concealing treatment allocation in randomised trials. Blinding in clinical trials and other studies. The odds ratio. How to randomise. Treatment allocation in controlled trials: why randomise?. Survival probabilities (the Kaplan-Meier method). Bayesians and frequentists. Time to event (survival) data. Generalisation and extrapolation. The intracluster correlation coefficient in cluster randomisation. Sample size in cluster randomisation. Weighted comparison of means. Analysis of a trial randomised in clusters” – http://bmj.bmjjournals.com/series/
- Probability and statistics resources: “This site presents access to the recent developments in computational methods, methodology for data analysis and their applications in construction of probabilistic and statistical modeling for decision making under risk that is of interest to researchers and graduate students across a number of academic domains.”- http://home.ubalt.edu/ntsbarsh/Business-stat/R.htm
- Statistical Genetics Humor Page: “The information collected here is dedicated to proving the following theorem: Theorem: All statistical geneticists are not humorless nerds! Unfortunately, the above theorem has been disproved – see here for the fatal counter-example! So we now have a revised theorem: Revised theorem: Not all statistical geneticists are humorless nerds!” – http://watson.hgen.pitt.edu/humor/
- Statistics links: “links for statistical calculations” – http://www.esf.edu/efb/gibbs/monitor/popmon%20statistics%20links.html
- Statistics resources: “Includes sections about Famous Statisticians, Free Software, Commercial Software, Books & Journals” – http://www.ulg.ac.be/cogsci/Links/Statistics.html
- Web Pages that Perform Statistical Calculations: “The web pages listed here comprise a powerful, conveniently-accessible, multi-platform statistical software package. There are also links to online statistics books, tutorials, downloadable software, and related resources. All of these resources are freely accessible, once you can get onto the Internet.” – http://members.aol.com/johnp71/javastat.html