Krona is now on GitHub, beginning with KronaTools 2.6. New releases can be found at https://github.com/marbl/Krona/releases.
-a) that include all Krona resources and require neither an internet connection or a local KronaTools installation to be viewed
ktImportTaxonomywill set invalid taxonomy IDs to root and produce a warning, rather than erroneously assigning them to "No hits".
ktImportBLASTwill warn about GIs with missing or invalid taxonomy IDs, rather than running forever.
-e) ineffective when computing the lowest common ancestor, causing classifications to be too generic. Bit scores are now used instead by default, with
-tspecifying the range for ties. The
-eoption is still available and may be useful for concatenations of BLAST output against various DBs, since e-values account for DB size.
install.pl) now works with Perl 5.14+.
-qpoption in any importer that uses query IDs.
-koption (previously these taxa were always collapsed). The taxonomy database has to be rebuilt with
updateTaxonomy.shbefore this option can be used.
ktImportRDPnow accepts the current format of the RDP Classifier web portal output (in addition to older formats).
ktImportRDPcould cause incorrect rank information to be shown when importing "allrank" results from the web portal (rather than "fixrank"). Rank information will now be omitted when loading "allrank".
ktGetTaxIDFromGIwas added to translate GIs to taxonomy IDs.
-noption for specifying the name of the highest level.
-u) now display in Firefox.... read more
-d) to restrict the hierarchical depth that is shown in the chart.
-y) for specifying a custom hue range instead of the default red-green gradient.
ktImportMETAREP-ECwas added to create a profile of EC numbers in METAREP
ktImportECwas added to import tabular files containing EC numbers and, optionally, query IDs, magnitudes, and scores.
ktImportDiskUsagecan be used to show file and folder sizes.
ktImportTaxonomyusing column options.
ktClassifyBLASTnow reports classifications for each query, rather than summarizing by taxonomy ID. Summarized results can still be obtained using -s, but the output format has changed to: magnitude, taxID, score. Also, output files now begin with a comment line that lists the fields.
ktClassifyBLAST's new default output (queryID, taxID, score).
Charts must be created with KronaTools 2.0 or later to have these changes. Older charts will continue to work, but will not receive updates.