NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.
A number of smaller changes that ultimately improves the handling of datasets with shoddy annotation of species in the MCL test set. I've tried to include some error catching conditions and output useful error messages. If only one of two annotations is useful for cogeqc, an error won't be used, and the workflow proceeds with the remaining "good" annotation (i.e. orthogroups contain more than one species for which proteins have annotations from this source).
A number of smaller changes that ultimately improves the handling of datasets with shoddy annotation of species in the MCL test set. I've tried to include some error catching conditions and output useful error messages. If only one of two annotations is useful for cogeqc, an error won't be used, and the workflow proceeds with the remaining "good" annotation (i.e. orthogroups contain more than one species for which proteins have annotations from this source).