Bioinformatics

Paradis, Emmanuel

doi: 10.1093/bioinformatics/btp696pmid: 20080509

Summary: pegas (Population and Evolutionary Genetics Analysis System) is a new package for the analysis of population genetic data. It is written in R and is integrated with two other existing R packages (ape and adegenet). pegas provides functions for standard population genetic methods, as well as low-level functions for developing new methods. The flexible and efficient graphical capabilities of R are used for plotting haplotype networks as well as for other functionalities. pegas emphasizes the need to further develop an integrated–modular approach for software dedicated to the analysis of population genetic data.Availability: pegas is distributed through the Comprehensive R Archive Network (CRAN): http://cran.r-project.org/web/packages/pegas/index.html Further information may be found at: http://ape.mpl.ird.fr/pegas/Contact: [email protected]

Andorf, Carson M.; Lawrence, Carolyn J.; Harper, Lisa C.; Schaeffer, Mary L.; Campbell, Darwin A.; Sen, Taner Z.

doi: 10.1093/bioinformatics/btp556pmid: 20124413

Summary: Methods to automatically integrate sequence information with physical and genetic maps are scarce. The Locus Lookup tool enables researchers to define windows of genomic sequence likely to contain loci of interest where only genetic or physical mapping associations are reported. Using the Locus Lookup tool, researchers will be able to locate specific genes more efficiently that will ultimately help them develop a better maize plant. With the availability of the well-documented source code, the tool can be easily adapted to other biological systems.Availability: The Locus Lookup tool is available on the web at http://maizegdb.org/cgi-bin/locus_lookup.cgi. It is implemented in PHP, Oracle and Apache, with all major browsers supported. Source code is freely available for download at http://ftp.maizegdb.org/open_source/locus_lookup/.Contact: [email protected]