Validating an instrument
We welcome all code contributions, from helping to improve the code, fix bugs, improve usability, and improve documentation, which is rather sparse, at the moment.Please contact us through twitter (@ultraconserved) if you are interested in helping and/or post an issue on github for the respective package.Concatenates reads into an "interleaved" file for use with velvet.Report an issue with illumiprocessor Get illumiprocessor » A program started by Nick Crawford with contributions from Brant Faircloth for parallel computation of individual genetrees and the estimation of a species tree from gene tree data.Capable of demultiplexing hundreds of sequence tagged libraries at once. Get splitaake » A program for automated cleaning of fastq files from sequencing.Removes adapter contamination using scythe and trims reads for quality using sickle.
Order enrichment kits from MYcroarray » The linked FASTA file (ZIP archive) contains probe sequences (120 nt) designed for synthesis as part of a Agilent Sure Select or Mycro Array My Bait target enrichment kit.The resulting loci are the highly conserved that we target for use as molecular markers. 2009) probes that are similar in sequence to the UCE loci we are targeting. Here's a list of UCE-related talks at various conferences.These probe sets differ in number and composition, depending on the types of questions we are asking and the taxa with which we are working. Mc Cormack JE, Faircloth BC, Crawford NG, Gowaty PA, Brumfield RT, Glenn TC. Ultraconserved Elements Are Novel Phylogenomic Markers that Resolve Placental Mammal Phylogeny when Combined with Species Tree Analysis. Slides are available for each talk by clicking on the linked talk title.2007), suggesting that their role in the biology of the genome may be cryptic.You can identify UCEs in organismal genome sequences by aligning several genomes to each other, scanning the resulting genome alignments for areas of very high (95-100%) sequence conservation, and filtering on user-defined criteria, such as length (e.g., Bejerano et al. If you want to use these regions as genetic markers, it is best to remove UCEs that appear to be duplicates of one another which we loosely define as being in more than one spot within each genome that you aligned.
We have discovered (see Citations) that we can collect data from UCEs and the DNA adjacent to UCE locations (flanking DNA), and that these data are useful for reconstructing the evolutionary history and population-level relationships of many organisms. 2004) and we generally assume that UCEs must be important by the very nature of their near-universal conservation across extremely divergent taxa.