search

BDI-pathogens / phyloscanner

Phylogenetics between and within hosts at once, all along the genome.
GNU General Public License v3.0
47 stars 14 forks source link

Confusion of terminology "Trans" "Complex" #30

Closed evandiego closed 6 years ago

evandiego commented 6 years ago

Hi,

I am a little confused as to the meaning of trans, multi-trans and complex from the phyloscanner analyst trees program particularly in light of Thomas Leitner's papers on HIV. Are the ancestry types "Trans" equivalent to a combination of paraphyletic and polyphyletic (PP) while "multi-trans" equivalent to paraphyletic–monophyletic (PM) and complex is not indicative of direct transmission?

Or is there a better way using these programs to flush out these terms?

Thank you in advance. Evan

mdhall272 commented 6 years ago

Hi Evan,

"Trans" is PM. PP can resolve to either "multi-trans" or "complex". The key is whether, once the ancestral state reconstruction is done, all the state (host) changes are in one direction. If, whenever the states at the two ends of a branch differ, the parent state is A and the child B, then the classification is "multi-trans". If there are some A to B branches and some B to A branches, then it is "complex".

Thanks, Matthew

evandiego commented 6 years ago

Thanks Matthew for this clarification.