Ductape

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UPGRADE URGENCY: LOW, only a few improvements for BBH searches

FEATURES:
* dgenome start: two new options to modulate the BBH search
* -m to change the Blast scoring matrix (i.e. BLOSUM62)
* -e to change the Blast E-value threshold
* Slightly faster threads

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UPGRADE URGENCY: LOW, only a style fix has been added

BUGFIXES:
* dphenome rings: thicker categories legend

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UPGRADE URGENCY: LOW, the bug fixed in this version affects only users importing curve parameters from other softwares

BUGFIXES:
* dphenome start: bugfix when considering parameters with NAN values in all wells

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UPGRADE URGENCY: HIGH, some compounds were discarded in network reconstructions

FEATURES:
* dape start: new outputs to higlight relevant genome/phenome combinations
* pangenome: high genomic/phenomic variability are highlighted
* mutants: high phenomic variability in pathways w/ mutated genes are highlighted
* single organisms: all the genomic/phenomic data is showed

BUGFIXES:
* dape start: some compounds (w/ AV=0) were excluded from the network construction
* dape start: discard the analysis on the general pathways
* database: some queries have been optimized for pangenome analysis
* Other small bugfixes

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UPGRADE URGENCY: HIGH, the curve parameters extraction and clustering have been improved

FEATURES:
* dphenome start: slight changes to parameters calculation
* the smoothing algorithm is now less aggressive
* the recursive attempts on curve parameters estimation are reduced two
* dphenome start: clustering improvements
* the curve parameters are normalized prior to clusterization, in order to give all the parameters the same weight
* added a new option (-n) to set the number of clusters (and therefore tha maximum AV)

BUGFIXES:
* dape start: give the right number of distinct reaction IDs in the metabolic network tables
* Other small bugfixes and speed improvements

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UPGRADE URGENCY: LOW, if you work exclusively with DuctApe and use the standard bacterial PM plates

FEATURES:
* dphenome import-plates: the user can now analyze even custom plates
* the table in test/input/newplate.tsv contains an example
* dphenome add/add-multi: PM data analyzed by different programs (i.e. opm) can now be imported
* YAML/JSON file formats are supported
* Curve parameters calculated by other programs are considered: they may be overridden by using dphenome start -r
* dgenome export: PM data can now be exported in YAML/JSON format

BUGFIXES:
* dape init: if something goes wrong during DB creation raise an error
* Other small bugfixes