How do the linear instructions of the genome come to define the breath-taking complexity of animal bodies? Genes and proteins interact to control the expression phenotypes of cells, cells interact to specify tissue phenotypes, and tissues interact to form organs, which themselves interact to make bodies. And all these processes vary through the lifetime of an individual and through evolutionary time as species evolve.
How fast can evolution go? Why, if bacteria evolve 'faster' than humans, do they not 'win the race'? What determines rates of evolution: mutation, selection, genetic system, biological interactions?
If tissue X has 500 reads in 4000bp and tissue Y has 700 reads in 5000bp, are these the same?
Processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles.
README CRAN page
Phase haplotypes from genotypes based on a list of known haplotypes. Suited to highly diverse loci such as HLA.