KnuttBinPhylo is a pipeline to automatically construct a set of universal markers and use those to construct a phylogenetic tree.
Marker candidates are based on PFAM families and configured in the config file. The default candidates are based on the PhyloM sets A,B. Proteins from UniProt proteomes (Archaea and Bacteria) with this marker are downloaded and aligned using MAFFTs automatic run mode. Markers need to be present in 75% of proteomes across each domain (Bacteria, Archaea AND candidates). Proteomes then need to have 50% of the selected markers.
If a proteome contains has multiple proteins with the marker annotation, the JC distances from the candidates to a subsample(n=1000) of the other proteins with the marker will be calculated. If the identity is to low for the JC, an infinite distance is assumed. The candidate with the lowest median distance is selected.
After running the rule
refData the following files will be available:
The tree can be produced with the
tree rule. RAxML HPC is used, not the newer RAxML-NG as the tree will be calculated with rapid boostraps, this feature isn’t available in the newer implementation, but reduces the bootstraping time significantly.
For the 0.1 release the pipeline will provide files to annotate the tree in the iTOL tree viewer.