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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.Removes adapter contamination using scythe and trims reads for quality using sickle.Concatenates reads into an "interleaved" file for use with velvet.Please contact us through twitter (@ultraconserved) if you are interested in helping and/or post an issue on github for the respective package.

Capable of demultiplexing hundreds of sequence tagged libraries at once. Get splitaake » A program for automated cleaning of fastq files from sequencing.

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.

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.

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.

Capable of demultiplexing hundreds of sequence tagged libraries at once. Get splitaake » A program for automated cleaning of fastq files from sequencing.

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.

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.

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.

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.