v1.1.alpha08: major speedup for certain alignment types

18 Jun 2011, by Erick

The biggest news of this release is that columns of the alignment that don’t have an informative position in either the reference sequences or the query sequences get filtered out of the alignment. For alignments that have all of the query sequences in a fixed region of the reference alignment (e.g. PCR products for a given primer as is common for 16s surveys) this will reduce memory usage and initial start-up time by a significant factor.


  • Changed guppy tog to use polytomy instead of a _ delimiter joining sequence names.
  • guppy edpl now calculates the EDPL (expected distance between placement locations) for placements
  • The usual collections of minor improvements and fixes: see the CHANGELOG for more details.
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