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Data

[Supplementary information] and [VCF data] for Thomas et al. (2015): Full-genome evolutionary histories of selfing, splitting and selection in Caenorhabditis. Genome Research. 25: 667-678.

[Supplementary information] for Jovelin & Cutter (2011): MicroRNA sequence variation potentially contributes to within-species functional divergence in the nematode Caenorhabditis briggsae. Genetics. 189: 967-976.

[Additional Data] for Murray et al. (2011): Heritable determinants of male fertilization success in the nematode Caenorhabditis elegans. BMC Evolutionary Biology. 11:99. 

[Supplementary tables] for Cutter & Moses (2011): Polymorphism, divergence and the role of recombination in Saccharomyces cerevisiae genome evolution. Molecular Biology & Evolution. 28: 1745-1754.

[Supplementary information] for Cutter & Choi (2010): Natural selections shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae. Genome Research. 20: 1103-1111.

[Supplementary information] for Cutter & Agrawal (2010): The evolutionary dynamics of operon distributions in eukaryote genomes. Genetics185: 685-693.

[Supplementary data] for Reinke & Cutter (2009): Germline expression influences operon organization in the C. elegans genome. Genetics. 181: 1219-1228.

[Supplementary data] for Cutter et al. (2008): Patterns of molecular evolution in Caenorhabditis preclude ancient origins of selfing. Genetics. 178: 2093-2104.

[Supplementary tables] for Cutter (2008): Multilocus patterns of polymorphism and selection across the X-chromosome of Caenorhabditis remanei. Genetics. 178: 1661-1672.

[Supplementary tables] for Cutter (2008): Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate. Molecular Biology & Evolution. 25: 778-786.

[Supplementary figures] for Dolgin, Felix & Cutter (2008): Hakuna nematoda: genetic and phenotypic diversity in African isolates of Caenorhabditis elegans and C. briggsae. Heredity. 100: 304-315.

[Supplementary figures] for Cutter, Wasmuth & Blaxter (2006): The evolution of biased codon and amino acid usage in nematode genomes. Molecular Biology and Evolution. 23: 2303-2315.

[Supplementary table and figure] for Cutter (2006): Nucleotide polymorphism and linkage disequilibrium in wild populations of the partial selfer Caenorhabditis elegans. Genetics. 172: 171-184.

[Supplementary table] for Cutter et al. (2005): Transposable element orientation bias in the Drosophila melanogaster genome. Journal of Molecular Evolution. 61: 733-741.

[Supplementary figures] for Cutter & Ward (2005): Sexual and temporal dynamics of molecular evolution in C. elegans development. Molecular Biology and Evolution. 22: 178-188. 

[Supplementary table] for Cutter et al. (2003): Molecular correlates of genes exhibiting RNAi phenotypes in Caenorhabditis elegans. Genome Research. 13: 2651-2657.

 

Software

CodonsGamma17 calculates the maximum likelihood surface of g=4Nes for selection on preferred codons. It is a Perl script that evaluates polymorphism data based on the approach of McVean & Charlesworth (1999) as implemented in Cutter & Charlesworth (2006) and Cutter (2008). The accompanying zip file contains the Perl script, a limited documentation file, an example input file, and example output files.

CodonsGamma17.zip

 

Resources

We have compiled a customizable Google Map for many of the wild strains of Caenorhabditis species that we have in the lab, or that we have worked with previously. Our global map now includes strains for nearly 30 species. For a searchable database of many wild isolates, we recommend the Felix lab strain database.

Map of wild isolates for all Caenorhabditis species

We previously made individual species maps, which are now superceded by our integrated strain maping webpage. However, we include these links as a legacy. If you have a Google account, you can save the links to these maps to your account or import them into Google Earth. If you make maps for your strains, please let us know!

C. brenneri map of wild isolates 

C. briggsae map of wild isolates

C. elegans map of wild isolates

C. remanei map of wild isolates

C. sp. 5 map of wild isolates

C. sp. 9 map of wild isolates

 

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text & photos 2006-2016 by asher d. cutter. design 2006 by yee-fan sun