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We designed probes from UCEs by including flanking sequence from medaka.Because of the highly conserved nature of UCEs and their flanking sequence, we have found these probes work well across fishes.MYcroarray has even made a discounted "pilot" sized kit available for labs who want to do some test enrichments.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.Our main code repository for analyzing data collection from UCE loci.Contains command-line applications for assembling contigs from sequence data, finding which contigs align to UCEs, aligning UCE contigs, and preparing data for downstream analysis in mrbayes, raxml, and cloudforest. Get phyluce » A program for demultiplexing massively parallel sequencing reads tagged with edit distance or Hamming distance sequence tags - tailored to edit distance tags (see Tags).(2004) from David Haussler’s group and subsequently identified in several classes of organisms outside the group of original taxa (Siepel et al. The 27-way vertebrate genome alignment (Miller et al.2007) identified additional regions of high conservation.
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.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.Because UCEs are conserved across disparate taxa, UCEs are also That's an extremely good question, and one to which we do not entirely know the answer (Dermitzakis et al. UCEs have been associated with gene regulation (Pennachio et al. However, gene knockouts of UCE loci in mice resulted in viable, fertile offspring (Ahituv et al.