Protein coding HMMsfor Fungal Phylogenomics
This repository contains three sets of HMMs for Phylogenomic analyses. It is mostly intended to be used with PHYling which expects the folder structure in here and searches each of these HMMs against each species set of proteins.
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AFTOL_1 - Set of markers used by AFTOLI project
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AFTOL_70 - 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
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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
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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. This is generally the best marker set to use which balances a broad sampling of useful markers. In general these are pretty slowly evolving sequences but show enough diversification be phylogenetically informative for most comparisons at protein.
HMMs for the 1KFG project (1000 Fungal genomes: http://1000.fungalgenomes.org) and supports other pan-fungal phylogenetic analyses