UCEs were first described in a wonderful manuscript by Gil Bejerano et al.
(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.
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).
Capable of demultiplexing hundreds of sequence tagged libraries at once. Get splitaake » A program for automated cleaning of fastq files from sequencing.
Please contact us through twitter (@ultraconserved) if you are interested in helping and/or post an issue on github for the respective package.
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.Dropbox brings your files together, in one central place.They’re easy to find and safely synced across all your devices—so you can access them anytime, anywhere. Dropbox brings your files together, in one central place.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.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.Removes adapter contamination using scythe and trims reads for quality using sickle.