| ABItype | Reads files in ABI format |
| AlignmentAppearanceDialog | The class implementing the "Alignment appearance" dialog in the alignment module |
| aln_pos | Part of the ClustalW package |
| AutoAnnotate | Scans database(s) for known features in the current sequence |
| blastThread | A wxThreadHelper class to run BLAST queries in the background |
| CGdialog | This class contains the settings dialog for the CGviewer export function |
| CGview | This class manages the CGview export |
| ChildBase | The base class for all modules |
| cmd_line_data | Part of the ClustalW package |
| color | Part of the ClustalW package |
| EILB | The External Interface List Box class, a specialized wxHtmlListBox |
| EIpanel | The External Interface panel class |
| element | Part of the IPC package |
| ExternalInterface | The External Interface ChildBase class |
| FindSequenceDialog | The class implementing the "Find" dialog in various ChildBase modules |
| fit_dat | |
| GPOUT | Part of the IPC package |
| hept_pref | |
| ipc_compound | Part of the IPC package |
| isotope | Part of the IPC package |
| MatMenu | Part of the ClustalW package |
| MatMenuEntry | Part of the ClustalW package |
| menu_item | Part of the ClustalW package |
| MyApp | Application class |
| MyChild | The very, very, *very* important module to handle DNA in all its beauty! |
| myExternal | This class is a wrapper around HTTP GET commands |
| MyFrame | Frame class |
| MyFrameDropTarget | The class that handles drag'n'drop events for MyFrame |
| MySplitter | Specialized class based on wxSplitterWindow; used in MyChild to separate the different parts of the module |
| node | Part of the ClustalW package |
| panel_data | Part of the ClustalW package |
| PCR_troubleshoot_dialog | The class implementing the PCR troubleshooting dialog |
| PlasmidCanvas | The class to draw the DNA map, as well as the mini-map in the amino acid module |
| prettyopts | Part of the ClustalW package |
| ProgramOptionsDialog | The dialog containing program end enzyme global settings |
| range | Part of the ClustalW package |
| rangeNum | Part of the ClustalW package |
| ReadSeqVars | Part of the ClustalW package |
| SeqAA | Sequence display class showing amino acids |
| SeqAAstructure | Sequence display class showing amino acids |
| SeqABI | Sequence display class showing ABI sequencer peaks |
| SeqAlign | Sequence display class showing alignments |
| SeqBasic | The parent class for all sequence types, including DNA, amino acids, features, restriction sites, ABI peaks, etc |
| SeqBlank | Sequence display class showing a blank line |
| SeqDivider | Sequence display class showing a horizontal divider |
| SeqDNA | Sequence display class showing DNA |
| SeqFeature | Sequence display class showing annotated features |
| SeqNum | Sequence display class showing numbers "inline" |
| SeqPlot | Sequence display class showing plot data in the amino acid module |
| SeqPos | SeqPos manages the positions of all items for a single "type" (for example, DNA) |
| SeqPrimer | Sequence display class showing primers |
| SeqRestriction | Sequence display class showing restriction sites |
| SequenceCanvas | The main sequence display class |
| SequenceCharMarkup | This class contains the markup of a single character (borders, fore- and background) |
| SequencePartList | This class assists in the restriction site layout |
| SeriesMat | Part of the ClustalW package |
| spanel | Part of the ClustalW package |
| spec_points | Part of the IPC package |
| TAAProp | This class manages amino acid properties; so 20 total. Used by the static part of TVector |
| TABIviewer | The ABI (sequencer data) viewer module class |
| TAlignLine | Helper class for TAlignment; represents a line (a sequence) in the alignment |
| TAlignment | The alignment module class. Note: this is actually a child class of both ChildBase and wxThreadHelper! |
| TAlignmentDialog | The alignment settings dialog |
| TAminoAcids | The amino acid sequence display module |
| TAutoAnnotateDialog | The dialog class for the AutoAnnotate class/function |
| TCalculator | The calculator module |
| TClone | The CLONE format import/export class |
| TClone_Enzyme | Temporarily stores an enzyme |
| TClone_Gene | Temporarily stores an item |
| TCloneManager | |
| TCloningAssistant | The cloning assistant module |
| TCloningAssistantPanel | |
| TDDR | |
| TDDR_Timer | |
| Tdna2aa | This class stores a codon and the corresponding amino acid. Used by TVector |
| TEnzymeDialog | A dialog to display/edit enzyme properties |
| TEnzymeRules | Stores, loads, stores, and compares enzyme settings |
| TEnzymeSettingsTab | The "tab" for global and per-sequence enzyme/methylation/etc. settings |
| TextImportDialog | The dialog where one can enter a sequence manually |
| TFLAG | Helper class for ABItype |
| TFragment | A restriction fragment (from, to, length) |
| TGelLane | This class represents a lane on a virtual gel |
| TGenBank | GenBank format import/export class |
| TGenBankFeature | Helper class for TGenBank |
| TGraph | The graph drawing module |
| TGraphData | The class containing xy-data for graph drawing |
| TGraphDialog | |
| TGraphDisplay | The display class, containing graphs and scales; essentially, a "tab" |
| TGraphScale | The class containing a scale used in the graph |
| TGridBasic | The base class for each calculator submodule (grid/sheet) |
| TGridData | The codon table calculator submodule |
| TGridDNA | The DNA concentration/purity calculator submodule |
| TGridLigation | The ligation calculator submodule |
| TGridProtein | The protein concentration calculator submodule |
| TImageDisplay | The image display module |
| TIMGitem | Annotation drawing class |
| TIMGreader | This class can read the ancient BioRad IMG format (most of the time...) |
| TIPC | Part of the IPC package |
| TIPC_ELEMENT | Part of the IPC package |
| TIPC_PARS | Part of the IPC package |
| TIPCDialog | The dialog handling the TIPC settings |
| TItemEditDialog | Dialog to set item/feature color, offset, type etc.; called from TVectorEditor |
| TiXmlAttribute | |
| TiXmlAttributeSet | |
| TiXmlBase | |
| TiXmlBase::Entity | |
| TiXmlBase::StringToBuffer | |
| TiXmlComment | |
| TiXmlCursor | |
| TiXmlDeclaration | |
| TiXmlDocument | |
| TiXmlElement | |
| TiXmlHandle | |
| TiXmlNode | |
| TiXmlParsingData | |
| TiXmlText | |
| TiXmlUnknown | |
| TLigationDialog | The ligation dialog class |
| TMainTree | The main tree class |
| TMainTreeItem | Item in TMainTree |
| TManageDatabaseDialog | The database interface dialog; opening, storing, searching sequences |
| TMarkMem | This helper class of SequenceCanvas can memorize a marking of the sequences, and restore it |
| TMyDropTarget | Handles drag'n'drop events for items dragged between the two database lists in TManageDatabaseDialog |
| TMyGelControl | This class handles a single virtual gel for TVirtualGel, using TGelLane lanes |
| TMyImagePanel | This class represents the actual image displayed by TImageDisplay |
| TMyMultipleChoiceDialog | A dialog for multiple choices |
| TMySQLDialog | Creates the dialog for entering parameters to add a MySQL database |
| TOnlineTools | TOnlineTools class |
| TORF | This class manages open reading frames (ORFs) |
| TPDB | Can parse PDB files and generated annotated TVector sequences |
| TPhylip | |
| TPhyloTree | The phylogenetic tree module |
| TPhyloTreeBox | |
| TPrimer | This class holds and generates information about a primer |
| TPrimerDesign | The virtual PCR/primer design module |
| TPrimerDialog | The dialog to optimize primers |
| TProject | Project class |
| TProtease | Class to store a protease |
| TProteaseCut | Class to store a protease cut |
| TProteolysis | |
| TProteolysisGel | |
| TProteolysisSuggestion | |
| TPTree | |
| TransformSequenceDialog | Tiny dialog for transforming a DNA sequence |
| TREcache | Restriction enzyme site cache |
| TRestrictionCut | Stores a specific cut of a restriction enzyme |
| TRestrictionEditor | The restriction editor dialog class |
| TRestrictionEnzyme | Stores a restriction enzyme |
| TSantaLucia | The class implementing a "Santa Lucia" free energy set |
| tseqres | Helper class for TPDB, holds the TVector objects for each parsed PDB chain |
| TSequencingAssistantDialog | |
| TSequencingPrimerDialog | The dialog for settings when searching for sequencing primers |
| TSilmutDialog | Silent mutation dialog |
| TSilmutItem | Helper class for TSilmutDialog |
| TsiRNA | |
| TSpeakDialog | |
| TSQLresult | This class stores the results from SQL queries |
| TStorage | This is the famous storage class. It manages all MySQL and sqlite traffic |
| TTreeItem | Item in TVectorTree |
| TUndo | This class stores TVector objects for the undo function |
| TUReadSeq | This is a wrapper class for ureadseq, which can read many sequence formats |
| TURLtext | A text control highlighting URLs |
| TVector | This class stores all sequence information, both DNA and amino acids |
| TVectorEditor | The sequence edit dialog |
| TVectorItem | This class stores a vector item |
| TVectorTree | The vector items tree class |
| TVirtualGel | The virtual gel module |
| TXMLfile | This class is a wrapper around the tinyxml software, specialized for GenBankXML format |
| UserMatSeries | Part of the ClustalW package |
