Showing posts from July, 2013

PhyBin: tree binning by topology

Just submitted our first paper to PeerJ - the awesome new, open access journal aimed at tipping the entire publishing establishment on its head.  I'm looking forward to a smooth review process -- hopefully as sleek and helpful as the submission process. <UPDATE: our paper was accepted.  I will post a link to the paper once it's online!> Our manuscript presents PhyBin, a computer program aimed at binning precomputed sets of trees in Newick format, a file format produced by the majority of tree building software.  As we assert in the manuscript, PhyBin is a utility rather than a complete solution; it can serve as a component in many genomics pipelines, and provides a useful addition to the landscape of tools for dissecting and visualizing large numbers of trees.  After the user applies their chosen ortholog prediction and tree-building algorithms, PhyBin offers a quick way to visualize and browse the different evolutionary histories, either binned by topology and sorted b