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.
We have several larger probes sets in the works for fishes, and we are also working on optimizing probe sets based on their capture success, phylogenetic utility, etc. You can now buy this probe set direct from MYcroarray in the form of a capture kit.
MYcroarray has even made a discounted "pilot" sized kit available for labs who want to do some test enrichments.
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.
All computer code is available under a flexible open-source license (BSD).
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.Our main code repository for analyzing data collection from UCE loci.2007) identified additional regions of high conservation.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.