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.
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).
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 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.
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.
(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.
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.