Useful links:




Flybase BLAST

Department of Ecology and Evolutionary Biology

Lewis-Sigler Institute for Integrative Genomics

Drosophila simulans genome - A second generation assembly of the Drosophila simulans genome strain w501 ( using Illumina sequencing. Associated paper: Hu et al. 2012 Genome Research.

Insect Genomics - a database of RNAseq Illumina sequence data for 21 non-model insect species from three insect orders (Lepidoptera, Coleoptera and Hemitera). Associated paper: Zhen et al. 2012 Science.

Hybridization in Xiphophorus - scripts to simulate expected divergence under three coalescent models of speciation (allopatric speciation, speciation via admixture, and speciation with limited gene flow) in X. maculatus, X. hellerii, and X. clemenciae.  Associated paper: Schumer, Cui et al. 2013 Evolution.

Population genetic alignments for 200+ X-linked loci surveyed in D. melanogaster used in Callahan et al. 2011. Correlated evolution of nearby residues in Drosophilid proteins.  PLoS Genetics, 7(2): e1001315. [link]

Population genetic alignments for 105 X-linked loci surveyed in D. melanogaster and D. simulans.  Associated paper: Andolfatto P, Wong KM, Bachtrog D. 2010. Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species. Genome Biol Evol. 3:114-28. Epub 2010. [link].

Older stuff:

Sequences of D. melanogaster coding and non-coding data sets from Andolfatto Nature (2005).

Nexus files for mtDNA genes surveyed in Andolfatto et al. (2003) Evolution 57:305-316.

Nexus files and supplementary information for Andolfatto and Wall (2003) Linkage disequilibrium across a recombination gradient in African Drosophila melanogaster.

Nexus files of D. melanogaster and D. simulans polymorphism data sets analysed in Andolfatto and Przeworski (2000) and Przeworski et al.(2001), plus a few extra, can be downloaded here.