Make a plan to do a phylogenetic analysis on a functional level

Dill-PICL / GOMAP-Paper-2019.1

Data, code, and results for our paper Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants (https://doi.org/10.1093/gigascience/giac023). If you use any of our code or results in a scientific publication, we would be grateful if you cite the paper.

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Make a plan to do a phylogenetic analysis on a functional level #35

Closed Thyra closed 2 years ago

Thyra commented 5 years ago

What exactly do we want to do, how do we do it?

Current idea: Try to reproduce "tree of life" subtree of our species with functional annotations as input, do a distance based tree with NJ and 1-hF1 as the distance metric.

Thyra commented 5 years ago

1st and simplest idea: Aggregate all annotations genome-wide (pretend there was only 1 gene), remove duplicates, then do the hF1 and tree on that.

Thyra commented 2 years ago

done