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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.
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.
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.
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.Many of the steps, at this point, require that you are comfortable working with computer software on the command line. MYcroarray has even made a discounted "pilot" sized kit available for labs who want to do some test enrichments.We encourage everyone interested to get the software and contribute to the effort of documenting, improving, and extending our computer code. Order enrichment kits from MYcroarray » We designed probes from UCEs by including flanking sequence from chickens.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).
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.