New OMArk version compatible with OMAmer v 2.0.0.
Changes are:
- Due to changes in OMAmer, dubious proteins or proteins with no homologs now will tend to be placed as Unknown rather than Inconsistent.
- Slight changes to contamination detection module that account only for most significant hits and handle better close contaminants.
- Adding -r option that allows to gives a taxonomic rank as parameter (order, class, phylum) for ancestra lineage selection.
- Adding a warning when the clade chosen is subgenus or phylum and higher.
- Adding the -c options that only outputs a list of conserved HOGs for a given clade.
- Adding a new companion Notebook to contextualize OMArk results with OMA data (sequences, synteny).
- Adding new simulation for benchmarking (genome_simulation.py)
- Minor fix to setup.cfg and import of the Bio library