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bowmanjeffs / paprica

paprica - PAthway PRediction by phylogenetIC plAcement
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Change to multigene alignment #8

Closed bowmanjeffs closed 4 years ago

bowmanjeffs commented 8 years ago

Impossible to get truly "correct" reference tree topology without a multigene alignment. It should be possible to download covariance models for an appropriate subset of genes and make a multigene alignment. This would of course require two trees; one for placement based on multigene alignment and one for stats based on 16S only.

bowmanjeffs commented 7 years ago

5S + 23S + 16S

All (5S) http://rfam.xfam.org/family/RF00001

Archaea http://rfam.xfam.org/family/RF02540 http://rfam.xfam.org/family/RF01959

Bacteria http://rfam.xfam.org/family/RF02541 http://rfam.xfam.org/family/RF00177

Eukarya http://rfam.xfam.org/family/RF02543 http://rfam.xfam.org/family/RF01960