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Get protocols » The most complex part of using UCEs to understand evolutionary relationships, population structure, and population relationships is analyzing the DNA sequence data. Mc Cormack JE, Harvey MG, Faircloth BC, Crawford NG, Glenn TC, Brumfield RT. A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing. Generally speaking, these commercial vendors will accept DNA extracts for enrichment, conduct the library preparation and enrichment steps, sequence the enriched libraries, and return the sequence data to you. We are constantly evaluating the utility of given probe sets and probe designs, in addition to expanding the number of UCE loci we are targeting.
We have created several software packages and we're working on tutorials to help get you started. A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs). We do not derive any referall revenue from these companies, but we list each here to help interested labs get started. We have several larger probes sets in the works, and we are also working on optimizing probe sets based on their capture success, phylogenetic utility, etc. You can now buy each of these probe sets direct from MYcroarray in the form of a capture 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).
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.
Because of the highly conserved nature of UCEs and their flanking sequence, we have found these probes work well across amniotes. We are constantly evaluating the utility of given probe sets and probe designs, in addition to expanding the number of UCE loci we are targeting.
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.
As their name implies, ultraconserved elements (UCEs) are highly conserved regions of organismal genomes shared among evolutionary distant taxa - for instance, birds share many UCEs with humans.
UCEs were first described in a wonderful manuscript by Gil Bejerano et al.
Get 2,001 probe set for fish » Below are several software packages we have developed to help analyze data collected from UCE loci.
All computer code is available under a flexible open-source license (BSD).