Files in this directory include bait designs and standardized outgroup data from various sets of target enrichment probes used for collecting UCE data from tetrapod organisms (e.g. see [Fair:2012a]).
Probe designs, genomic positions of designed probes, fasta slices around genomic positions of designed probes, and outgroup UCE loci generated from fasta slices are avaialable for various sets of baits.
You are free to use these data in your analyses. If you use the bait designs or outgroup data here, please reference [Fair:2012a] and this website. You can provide the version of the data you used or provide the hash of the commit you used in the text of your manuscript, if so desired.
All of the genomic data used to generate these files are available publicly. You should reference the source of a given genomic build in your Literature Cited. A good list to find all of these sources is available by finding a given build on the UCSC Genome Browser and looking at the build details.
| [Fair:2012a] | (1, 2, 3) Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC (2012). Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales. Systematic Biology 61: 717-726. pmid: 22232343 doi: 10.1093/sysbio/SYS004. |
The tetrapod bait designs in this repository are available as commercially produced "capture-kits" from Arbor Biosciences.
This repository is organized into V1 and V2 directories. The V1 directory includes "older" bait design files that were described in [Fair:2012a]. There is a README file within this directory describing its structure.
The V2 directory includes "newer" bait design files where we have updated the V1 bait set to remove underperforming loci, standardized bait number per locus (to 2 or 4), provided one design for enriching "high-quality" sequencing libraries (5kV2A) and another design for enriching "low-quality" sequencing libraries (5kV2B). The V2 bait set is largely an improvement on V1, although these particular files have been especially tailored for working with birds.
Files in this directory are version controlled, so if you are looking for earlier outgroup data sets, please click the tags_ link above to access these earlier versions.
Minor changes to the text of these documents or additional of explanatory details will generally result in a minor version bump (e.g., v3.0 to v3.1). Major changes to the contents of the repository (due to error or addition of new probes/taxa) will result in a major version bump (e.g., v3.0 to v4.0).
