v1.1.alpha11: Bugfix and minor improvements

18 Dec 2011, by Erick

This is mostly a bugfix release. The most significant fixed problem was that placing on a FastTree tree could fail when when using a combined reference + query alignment.

Also * EDPL coloring for fat trees is back * guppy pca can now be done in an unweighted fashion * All commands that work on reference packages now use the -c flag for consistency * Terminology change: ‘weighted’ -> ‘spread’ and ‘unweighted’ -> ‘point’ * Having some unclassified sequences now works fine in reference packages

There are a bunch of other minor fixes and changes; see the CHANGELOG for more details.

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