Table 1.
Pathway Tools capabilities introduced since Pathway Tools 19.0 (2015)
| Capability | Discussed in section | Web or Desktop |
|---|---|---|
| New search capabilities | PGDB Management | Both |
| GFF3 and Genbank export enhancements | PGDB Management | Desktop |
| Search for pseudogenes and cryptic prophages | PGDB Management | Web |
| Changed pseudogene representation | PGDB Management | Both |
| Show regulation details in pathway pages | PGDB Management | Both |
| Improved graphics and fonts | PGDB Management | Web |
| Revised protein feature coloring | PGDB Management | Both |
| Sequence coordinate mapping service | PGDB Management | Web |
| Redesigned gene pages | PGDB Management | Web |
| Redesigned metabolite pages | PGDB Management | Web |
| Notification of database updates | PGDB Management | Web |
| Scalability and performance | PGDB Management | Both |
| Multi-organism route search | Pathway Informatics | Web |
| Pathway prediction algorithm extended | Pathway Informatics | Desktop |
| SBML export | MetaFlux | Desktop |
| FVA | MetaFlux | Desktop |
| MetaFlux web solving mode | MetaFlux | Web |
| Send model fluxes to Dashboard | MetaFlux | Both |
| Send model outputs to GNUplot | MetaFlux | Desktop |
| Improvements to MetaFlux gap filler | MetaFlux | Desktop |
| Community models occupy spatial grid | MetaFlux | Desktop |
| Pathway covering | Omics Analysis | Web |
| Multi-omics explainer | Omics Analysis | Desktop |
| Omics Dashboard | Omics Analysis | Both |
| Import data from Metabolomics Workbench | Omics Analysis | Desktop |
| PPS | Omics Analysis | Web |
| Pathway collages | Omics Analysis | Both |