Gene tools

There are many tools used for genetic data analysis. Discussed here are resources where some of these tools can be found.

Description

Genetics data is quite distinct and many programs have been developed to assist with its analysis. Some programs are multi-purpose, while others are highly specialised. Below is a selection of resources that include links to, and synopses and reviews of, many genetic analysis programs.

1. NCBI Tools for Data Mining (http://www.ncbi.nlm.nih.gov/Tools/). Tools have been developed for nucleotide and protein sequence analysis, structures, gene expression, and for genome analysis.
2. An Alphabetic List of Genetic Analysis Software (http://linkage.rockefeller.edu/soft/list1.html). Over 400 programs include genetic linkage analysis, QTL analysis for animal/plant breeding data, genetic marker ordering, genetic association analysis, haplotype construction, pedigree drawing, and population genetics. 1
3. Resources for Ecology, Evolutionary Biology, Systematics, and Conservation Biology (http://darwin.eeb.uconn.edu/links/category.php?id=12). Of the many categories of resources here, there are links to molecular evolutionary software.
4. Genetic Data Analysis (http://gallus.forestry.uga.edu/dataAnalysis/) The emphasis is on analysis/generation of genetic data using maximum likelihood or Bayesian estimation of parameters of interest.2
5. The Gene Ontology - Tools for Gene Expression Analysis (http://www.geneontology.org/GO.tools.microarray.shtml). Software developed to use the gene ontologies or gene associations provided by GO consortium members.
6. GSF - The Genetic Software Forum (http://www.rannala.org/gsf/). Discussion lists, Q&A, and articles about genetic software
7. A recent review paper which describes the principles, the statistics computed, the assumptions made, and some limitations, is: Excoffier L & Heckel G (2006) Computer programs for population genetics data analysis: a survival guide. Nature Reviews Genetics 7: 745-758, (October 2006).

Function

• Analysis tools

Why use this tool?

• Genetics analyses

Who will use this tool?

• Data users
  • Expert
  • Interest groups
• Special skills are required

How will the tool be used?

Flow chart of possible data exchange between different population genetics programs. Although many programs have their own input-file specification, data files can still be exchanged between most programs (black arrows), avoiding tedious reformatting processes. The red stars are recommended starting points to format an initial data set. Blue ellipses represent multi-purpose packages, whereas individual-centred programs are shown in violet. The two conversion programs are shown in yellow. Specialized programs are shown in green, and light grey ellipses represent programs … the data formats of which are used by other programs allowing indirect data exchange (white arrows). The data files associated with the programs listed on the bottom row cannot be exchanged directly with the other programs.3

• Online and desktop applications
• Available for many different platforms
• User input is required

Where in the data chain could this tool be used?

• User’s machine

When could this tool be used?

• As a post process, after data is with the user

Availability

• NCBI Tools for Data Mining: http://www.ncbi.nlm.nih.gov/Tools/
• Alphabetic List of Genetic Analysis Software: http://linkage.rockefeller.edu/soft/list1.html
• Resources for Ecology, Evolutionary Biology, Systematics, and Conservation Biology:  http://darwin.eeb.uconn.edu/links/category.php?id=12
• Genetic Data Analysis: http://gallus.forestry.uga.edu/dataAnalysis/
• The Gene Ontology: http://www.geneontology.org/GO.tools.microarray.shtml
• GSF - The Genetic Software Forum: http://www.rannala.org/gsf/
• Many genetics analysis programs are freely available

Comments

• Rather than manipulate genetics data specifically, the ALA could probably act as a conduit or link between the source and the user.
• This list of resources is by no means complete.