This HMM database is trained from the latest ARB database release.
It contains profile hidden Markov models for all taxa represented in the ARB Silva database, release 108, trained using the default settings of hmmbuild.
This is the taxonomic index for SSUMMO release 108, with all training sequence accessions removed.
To update your existing SSuMMo installation, configure CONFIG.py to use this file instead of the old taxIndex.
Settings like `top' and `arbDBdir' need to be configured appropriately. Please see CONFIG.py for full details.
This contains the complete taxonomic index for SSUMMO release 108, with each training sequence accession assigned to the appropriate taxon.
This is unnecessary for SSuMMo usage, but is needed when building the HMMs with dictify.py.
This contains all the models as the above database, but these models were trained by giving the option '--wgiven' to hmmbuild. The difference is that by default, hmmbuild does some clever sequence weighting using prior probabilities. By giving the --wgiven option, hmmer does no prior weighting and so the HMMs here hold expected probabilities calculated directly from the observed training sequences.
These are the mysql dumps for the taxonomy databases. They contain a minimised version of the NCBI taxonomy database, and tables which relate each taxon found in the ARB database to the NCBI taxonomic IDs and the ranks for each taxon, where found.
md5 digest - 6498426cbd9043f0d3fc15d5ae8875db
Department of Biology University of York,