Locally-developed tools

• Blast Parser

• Contig Viewer

  Py_ContigViewer is a contig viewer, a stand alone cross-platform desktop application that uses CAP3 alignments to graphically display and validate candidate SNPs and InDels. It also simplifies PCR oligo design in an interactive mode. The extended mode provides the display of BLAST hits of annotated sequences with intron positions for the selected contig. Py_ContigViewer works in conjunction with DIS (Deletion, Insertion, Substitution) SNP discovery pipeline at http://cgpdb.ucdavis.edu/SNP_Discovery/.

• Genome Pixelizer

  GenomePixelizer was designed to help in visualizing the relationships between duplicated genes in genome(s) and to follow relationships between members of gene clusters. GenomePixelizer may be useful in the detection of duplication events in genomes, tracking the "footprints" of evolution, as well as displaying the genetic maps and other aspects of comparative genetics.

• Genoplayer

  A program for visualizing and querying genetic data.

• PhyloGrapher

  PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements). PhyloGrapher is a drawing tool that generates custom graphs for a given set of elements. In general, it is possible to use PhyloGrapher to visualize any type of relations between elements.

• SNP discovery pipeline

Other useful bioinformatics links

• Bioinformatics.org

• Open source bioinformatics software (from freshmeat.net)

• The Cartwheel Project (from CalTech)

  Web-based sequence analysis tools.