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This Week in Nucleic Acids Research: May 8, 2019

Researchers in Germany present an Automated Multi-Locus Species Tree, or AutoMLST, approach for developing multi-locus sequence analysis (MLSA)-based bacterial trees in an automated manner. The pipeline is meant to serve as speedy, "one-click" method for coming up with bacterial species trees with MLSA, the team notes, while reportedly offering greater species resolution and a more refined look at bacterial evolutionary relationships compared with analyses of 16S ribosomal RNA gene sequences alone. "The resulting phylogenetic tree also includes helpful annotations, such as species clade designations and secondary metabolite counts to aid natural product prospecting," the authors explain, adding that the automated method "enables a wide range of researchers to perform rigorous phylogenetic analyses more rapidly compared to manual MLSA workflows."

A team from the US and China describes the chromatin state sequence comparison tool EpiAlign. The alignment-based bioinformatics approach relies on a dynamic programming algorithm to bring together "varying lengths and frequencies of chromatin states" as a means of comparing and finding local chromatin alignments for "multi-track epigenomic signals," the researchers note. They subsequently used EpiAlign to find chromatin state patterns — including some cell-type specific epigenomic features — in simulated data and real data from embryonic stem cell, heart, and brain samples profiled for the National Institutes of Health Roadmap Epigenomics effort.

Finally, researchers from China's Southwest University, the University of California at Berkeley, and the US Department of Agriculture's Agricultural Research Service outline the latest version of an online genome comparison platform called OrthoVenn2. The updated version of the platform is designed for comparing orthologous clusters in as many as a dozen species based on whole-genome sequence data, the team explains, and includes tools for visualizing and interpreting data. "To facilitate a broader range of comparisons, a larger number of species, including vertebrates, metazoan, protists, fungi, plants, and bacteria, have been added in OrthoVenn2," the investigators write, noting that a "stand-alone version is available to perform large dataset comparisons and to visualize results locally without limitation of species number."