Pathway Tools File FormatsThis page documents file formats for input files accepted by Pathway Tools, and for output files generated by Pathway Tools.
Input File Formats for Building New Pathway/Genome DatabasesGiven an annotated genome as input, Pathway Tools constructs a new Pathway/Genome Database containing the input genome plus new computationally inferred information such as the metabolic network of the organism. Here we list the input formats accepted by Pathway Tools with various commentary about these formats.
Overall we recommend GFF3 format because a single GFF3 file can contain all sequence plus annotation for a genome with multiple replicons, and because we have observed problems with representation of alternative splicing in GenBank-format files.
Other Input File Formats
Input File Formats
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