** The data for Baker et al. ‘Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates’ (2017) are available as:
** The data for Moorjani, Amorim et al. ‘Variation in the molecular clock in primates’ (2016) are available as:
- Multiple sequence alignment of 10 primates: Multiz.tar.gz
- Multiple sequence alignment of 7 primates: EPO.tar.gz
- Details of the data processing: README
- Figures and associated data: github
** The data for Singhal, Leffler et al. ‘Stable recombination hotspots in birds’ (2015) are available as:
- Aligned sequence reads (as BAM files) for zebra finch, long-tailed finch, and double-barred finch at http://www.ebi.ac.uk/ena/
- Filtered variant call data (as VCF files) for zebra finch, long-tailed finch, and double-barred finch at http://www.ebi.ac.uk/ena/
- RNAseq data for zebra finch testes at http://www.ncbi.nlm.nih.gov/
- Ancestral genome reconstruction for zebra finch, long-tailed finch, and double-barred finch at DataDryad: doi:10.5061/dryad.fd24j
- Masked genome files for zebra finch, long-tailed finch, and double-barred finch at DataDryad: doi:10.5061/dryad.fd24j
- Raw recombination output from LDhelmet for zebra finch and long-tailed finch at both block penalties 5 and 100 at DataDryad: doi:10.5061/dryad.fd24j
- Scripts and labnotebook at https://github.com/singhal/
postdoc and https://github.com/singhal/ labnotebook, respectively
- All other data can be requested via e-mail from sonal [dot] singhal1 [at] gmail [dot] com
** TroX: a R package for Kermany et al. (2014)
** Shared SNP coordinates for Leffler et al. (2013) Science.
** Table S1 for Meyer et al. (2012) Genetics.
** For the data reported in Auton et al. (2012) Science:
The sequence data (in BAM file format), variant calls (in VCF file format), genetic maps, and sequenced PRDM9 alleles are available for download over anonymous FTP from ftp://birch.well.ox.ac.uk/. The BAM files are available from the Short Read Archive,
Given the large number of repeat classes, we do not show recombination rates around all possible repeats in our paper. However, recombination rates around any repeat with more than 200 occurrences (after thinning nearby copies) of interest can be viewed using an interactive online viewer. The viewer can be accessed here.
** Supplementary Material S2 for Fledel-Alon et al. (2011) PloS One.
** Kevin Bullaughey’s regulatory evolution simulation software (Changes in selective effects over time facilitate turnover of enhancer sequences) described in Bullaughey, K. (2011) Genetics, is available here.
** Ryan Hernandez’s SFS_CODE (Selection on Finite Sites under Complex Demographic Effects), described in Hernandez (2008) Bioinformatics is available here.
** Supplementary materials for Coop et al. (2008) Science.
** Carole Ober’s website on mapping in the Hutterites:http://www.genes.uchicago.edu/hutterite/home.html
** Supplementary materials for Teshima et al. (2006) Genome Research: PDF file.
** For the program described in Przeworski et al. (2005) Evolution, SELSIMSTAND, contact Graham Coop.
** Supplementary materials for Ptak et al. (2004) Genetics: PDF file.
** Program described in Przeworski (2003) Genetics, available upon request to Molly Przeworski (mp3284 at columbia.edu).
** Supplementary materials for Ptak and Przeworski (2002) TIG: Tab-delimited text file.