Update README.md

README.md

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-# fungal_PHYling_HMMs
-PHYling HMM datasets for Fungi
+# Proein coding HMMsfor Fungal Phylogenomics
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+This repository contains three sets of HMMs for Phylogenomic analyses. It is mostly intended to be used with [PHYling](https://github.com/stajichlab/PHYling_unified) 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
+* 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
+* 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. 
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+HMMs for the 1KFG project (1000 Fungal genomes: http://1000.fungalgenomes.org) and supports other pan-fungal phylogenetic analyses