| File/Module | Location | Description |
| BlastProDom.pm | iprscan/lib/Dispatcher/Tool | ProDom output parser |
| Coils.pm | iprscan/lib/Dispatcher/Tool | Coils output parser |
| Config.pm | iprscan/lib/Dispatcher | Interface to configuration files |
| FAQs | iprscan/doc/html | FAQs file |
| Fasta.pm | iprscan/lib/Index | Fasta sequence file indexing utilities |
| FingerPrintScan.pm | iprscan/lib/Dispatcher/Tool | Prints output parser |
| Gene3DPostFilter.pm | iprscan/lib/Dispatcher/Tool/Hmmer | Gene3D output parser |
| HAMAP.pm | iprscan/lib/Dispatcher/Tool | HAMAP output parser |
| HMMPIR.pm | iprscan/lib/Dispatcher/Tool | PIR output parser |
| HMMPanther.pm | iprscan/lib/Dispatcher/Tool | Panther output parser |
| Hmm.pm | iprscan/lib/Index | HMM models information; searching utilities |
| Hmm3.pm | iprscan/ | |
| Hmmer.pm | iprscan/lib/Dispatcher/Tool | Hmmer applications output parser |
| Hmmer3.pm | iprscan/ | |
| Index.pm | iprscan/lib | Generic indexing utilities |
| InterPro.pm | iprscan/lib/Index | InterPro information; searching utilities |
| InterProScan.pm | iprscan/lib/Dispatcher/Tool | InterProScan utilities |
| InterProScanParser.pm | iprscan/lib/Dispatcher/Tool | InterProScan xml output parser |
| IprMatches.pm | iprscan/lib/Index | IprMatches information; searching utilities |
| Logger.pm | iprscan/lib | |
| PatternScan.pm | iprscan/lib/Dispatcher/Tool | PatternScan output parser |
| PfamA.pm | iprscan/lib/Index | Pfam-A.seed file information; searching utilities |
| PfamClan.pm | iprscan/lib/Index | Pfam Clan file information; searching utilities |
| PfamPostFilter.pm | iprscan/lib/Dispatcher/Tool/Hmmer | Pfam output parser |
| Prints.pm | iprscan/lib/Index | Prints information; searching utilities |
| ProDomBlast3i.pl | iprscan/bin | ProDom application launcher |
| ProfileScan.pm | iprscan/lib/Dispatcher/Tool | ProfileScan output parser |
| Queue.pm | iprscan/lib/Dispatcher | Interface to queuing systems |
| README | iprscan/doc/html | README file |
| ResubmitJobs.pl | iprscan/bin | Failed jobs resubmiting script |
| ScanRegExp.pm | iprscan/lib/Dispatcher/Tool | ScanRegExp output parser |
| Seg.pm | iprscan/lib/Dispatcher/Tool | Seg output parser |
| SignalP.pm | iprscan/lib/Dispatcher/Tool | SignalP output parser (v1.X and higher) |
| SmartDesc.pm | iprscan/lib/Index | Smart descriptions information; searching utilities |
| SmartOverlaps.pm | iprscan/lib/Index | Smart overlaps information; searching utilities |
| SmartPostFilter.pm | iprscan/lib/Dispatcher/Tool/Hmmer | Smart output parser |
| SmartThresholds.pm | iprscan/lib/Index | Smart thresholds information; searching utilities |
| SuperFamily.pm | iprscan/lib/Dispatcher/Tool | SUPERFAMILY output parser |
| TMHMM.pm | iprscan/lib/Dispatcher/Tool | TMHMM output parser |
| Tool.pm | iprscan/lib/Dispatcher | Base class for tools |
| index_data.pl | iprscan/bin | Indexing script for data files |
| iprscan_wrapper.pl | iprscan/bin | InterProScan wrapper script |
| meter.pl | iprscan/bin | Percentage of jobs done |
| ps_scan.pl | iprscan/bin | ProfileScan application launcher |
| wget.pl | iprscan/bin | Indexes status checker and informations retriever |