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Upgrading the way we deal with single-copy gene collections #401
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Special thanks for preparing this go to Mike Lee.
This new addition to the kind.txt will make it easier to recognize different classes of single-copy core genes.
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Although it has been extremely useful, the use of bacterial single-copy core genes has been a limiting factor to identify arcaheal bins easily from the interface.
Here is a complete revamp of the way we estimate the completeness of a given group of splits.
With this change the number of default SCGs for bacteria goes down to two (we retain only Alneberg et al and Campbell et al), and a new SCG becomes available for archaeal organisms (Rinke et al). Mike Lee had made this very important contribution, which in fact convinced us the importance of improving this: http://merenlab.org/2016/05/21/archaeal-single-copy-genes/ --so the anvi'o developers thank him very much for that :)
I am committing this pull request now, but I will extend the technical description of what happened later.