Three sets of HMMs for Phylogenomic analyses:
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JGI_1086 - A set of markers identified by the JGI as part of Mycocosm database. These are generally pan-fungal markers but are not fungal-specific. These are generally the most useful for phylogenomics but do incur more computational burden.
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AFTOL70 - set of markers used by the AFTOLII project for Phylogenomics chosen by phylogenetic informativeness. Mostly selected from an Ascomycete orthology analyses. First published in Floutas et al 2012 DOI: 10.1126/science.1221748
They work well in many instances but in some cases are less useful in resolving phylogeny than the JGI1086.
- Roz200 - Set of 192 markers selected from a Kindgom-wide analysis as part of Rozella genome analyses James et al 2013 DOI: 10.1016/j.cub.2013.06.05