v1.1.alpha09: many new features and fixes

18 Oct 2011, by Erick

This release was a long time coming, and it’s a doozy: 63 closed issues and 480-ish commits. The changelog entry is 200 lines, so I’m not going to go over all of it here. Here are some highlights:

• There are now three binaries, with rppr being the new kid. rppr stands for Reference Package PReparer, and it consequently has functionality that is relevant for working with reference pacakges.
• Version 2 of the JSON placement format.
• There is now a way of keeping all of your placements in one placefile but splitting them apart in various ways, see the guppy docs on ‘split’ placefiles for that. There may be a bit of a learning curve but it’s proven very useful for us.
• Virtual placefiles and command line substitution in batch files.
• It’s now possible to have a named mass rather than a list of names associated with a collection of placements.
• guppy mft is a new command for transforming these masses.
• Classification is our latest version, but we’re still tweaking it, so stay tuned.
• rppr convexify describes phylogeny/taxonomy discordance and rppr reroot does taxonomic rooting, as described in the corresponding paper.

For those of you who are compiling from source, there is a new version of the installation script. We’ve upgraded to OCaml 3.12 and started using the Batteries library, and this script will bring things up to date.

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