Month: November 2024

USEARCH 64-bit is now FREE!

In June 2024 Robert Edgar donated binaries for versions 5 through 11 of USEARCH to the public domain. You can now download them for free, including the 64-bit versions that used to cost $1,500, from this GitHub repository. At the same time USEARCH version 12 was launched as an open-source project at https://github.com/rcedgar/usearch12. See this paper announcing the open-source project.

Reference

Zhou Y, Liu YX, Li X. 2024. USEARCH 12: Open-source software for sequencing analysis in bioinformatics and microbiome. Imeta 3:e236.

RDP Website Discontinued

After more than 30 years in one form or another, the RDP website is no more. The server has died, the code is old, funding is exhausted, staff have retired or moved on. Developed in the pyrosequencing era, the pipeline tools are overwhelmed by today’s larger Illumina data sets.

The website is survived by the stand-alone version of the RDP Classifier available on Sourceforge and the command line version of RDP Tools. The later can be installed following the instructions on this website and here. Knowing there are still users of FunGene, we were hoping to find someone to host it, but so far with no takers. We have a nearly functional Amazon machine image of FunGene that could be used to build new gene models for Xander. If you are interested in using it or taking over FunGene, please leave a comment or email me (see the contact page).