SPHINX | Homology-Based Taxonomic

[…] s are MEGAN [], CARMA [], Sort-ITEMS [] or MetaPhyler [] that use similarity searches, the faster PhyloPythia [] or TETRA [] that use taxonomy-fitted nucleotide or codon usage composition analysis or SPHINX that uses a combination of the two [].A number of models have already been published [] by integrating known interactions (e.g. reagent/product at the enzyme level) from pathway repositories su […]

[…] r more so than when using other methods.Programs that primarily utilize sequence composition models include Naive Bayes Classifier (NBC) [,], PhyloPythia [,], PhymmBL [], RAIphy [], RDP [], Scimm [], SPHINX [], and TACOA []. Methods for building sequence models often make use of interpolated Markov models (IMMs), naive Bayesian classifiers, and k-means/k-nearest-neighbor algorithms. There is some […]

[…] nces having at least 80% identity (spread over at least 80% of the length) to human sequences were removed from subsequent analyses.All reads in both data sets were taxonomically classified using the SPHINX algorithm []. Analysis of these assignments at various taxonomic levels was performed by first collapsing all assignments at a desired taxonomic level, and subsequently enumerating the number o […]