In this section we have created a table of all of the AUTO CLUI commands, their abbreviations, and a one line description of what function they perform. Each command may be entered using its full name or any of its aliases.
| Command | Aliases | Description |
| commandAppend | ap append | Append data files. |
| commandCat | cat | Print the contents of a file |
| commandCd | cd | Change directories. |
| commandClean | clean cl | Clean the current directory. |
| commandCopyAndLoadDemo | dm demo | Copy a demo into the current directory and load it. |
| commandCopyDataFiles | copy cp | Copy data files. |
| commandCopyDemo | copydemo | Copy a demo into the current directory. |
| commandCopyFortFiles | sv save | Save data files. |
| commandCreateGUI | gui | Show AUTOs graphical user interface. |
| commandDeleteDataFiles | delete dl | Delete data files. |
| commandDeleteFortFiles | df deletefort | Clear the current directory of fort files. |
| commandDouble | double db | Double a solution. |
| commandInteractiveHelp | man help | Get help on the AUTO commands. |
| commandLs | ls | List the current directory. |
| commandMoveFiles | move mv | Move data-files to a new name. |
| commandParseConstantsFile | cn constantsget | Get the current continuation constants. |
| commandParseDiagramAndSolutionFile | bt diagramandsolutionget | Parse both bifurcation diagram and solution. |
| commandParseDiagramFile | dg diagramget | Parse a bifurcation diagram. |
| commandParseSolutionFile | sl solutionget | Parse solution file: |
| commandPlotter | p2 pl plot | 2D plotting of data. |
| commandPlotter3D | plot3 p3 | 3D plotting of data. |
| commandQueryBranchPoint | br bp branchpoint | Print the ``branch-point function''. |
| commandQueryEigenvalue | eigenvalue ev eg | Print eigenvalues of Jacobian (algebraic case). |
| commandQueryFloquet | fl floquet | Print the Floquet multipliers. |
| commandQueryHopf | hb hp hopf lp | Print the value of the ``Hopf function''. |
| commandQueryIterations | iterations it | Print the number of Newton interations. |
| commandQueryLimitpoint | lm limitpoint | Print the value of the ``limit point function''. |
| commandQueryNote | nt note | Print notes in info file. |
| commandQuerySecondaryPeriod | sc secondaryperiod sp | Print value of ``secondary-periodic bif. fcn''. |
| commandQueryStepsize | ss stepsize st | Print continuation step sizes. |
| commandRun | r run rn | Run AUTO. |
| commandRunnerConfigFort2 | changeconstant cc ch | Modify continuation constants. |
| commandRunnerConfigFort12 | hch | Modify HomCont continuation constants. |
| commandRunnerLoadName | ld load | Load files into the AUTO runner. |
| commandRunnerPrintFort2 | pc pr printconstant | Print continuation parameters. |
| commandRunnerPrintFort12 | hpr | Print HomCont continuation parameters. |
| commandShell | shell | Run a shell command. |
| commandSpecialPointLabels | splabs | Return special labels. |
| commandTriple | tr triple | Triple a solution. |
| commandUserData | us userdata | Covert user-supplied data files. |
| commandWait | wait | Wait for the user to enter a key. |