##
Directories

The files of the toolbox are organized in the following 23 directories

- BranchPoint
  Here are all files stored needed to do a branch point continuation. This includes the initializers and a branch point curve definition file. BranchPoint and BranchPointCycle are the only continuation curve types with three free system parameters in MATCONT.
- BranchPointCycle
  Here are all files stored needed to do a branch point of cycles continuation. This inluded the initializers and branch point of cycles definition files. BranchPoint and BranchPointCycle are the only continuation curve types with three free system parameters in MATCONT.
- Continuer
  Here are all the main files stored for the continuer, which are needed to calculate and plot any curve.
- Equilibrium
  Here are all files stored needed to do an equilibrium continuation. This includes the initializers and the equilibrium curve definition file.
- GUI
  This directory contains all GUI-related files. However, some files in this directory are also used in CL/SMALL>_MATCONT.
- Help
  Contains the help-files.
- Heteroclinc
  Here are all files stored needed to do a continuation of heteroclinic orbits. This includes the initializers and the curve definition file.
- Homoclinic
  Here are all files stored needed to do a homoclinic-to-hyperbolic-saddle continuation. This includes the initializers and the curve definition file.
- HomoclinicSaddleNode
  Here are all files stored needed to do a homoclinic-to-saddle-node continuation. This includes the initializers and the curve definition file.
- HomtopyHet
  Here are all files stored needed to find a heteroclinic connection by the homotopy method.
- HomotopySaddle
  Here are all files stored needed to find an orbit homoclinic to saddle by the homotopy method.
- HomotopySaddlenode
  Here are all files stored needed to find an orbit homoclinic to saddle-node by the homotopy method.
- Hopf
  Here are all files stored needed to do a Hopf point continuation. This includes the initializers and the Hopf point curve definition file.
- LimitCycle
  Here are all files stored needed to do a limit cycle continuation. This includes the initializers and the limitcycle curve definition file.
- LimitCycleCodim2
  This directory contains the routines that compute the normal form coefficients of codim2 bifurcations of limit cycles. Computing these coefficients reliably requires that computations are done to high precision and symbolic derivatives up to fifth order are used.
- LimitPoint
  Here are all files stored needed to do a limitpoint continuation. This includes the initializers and the limitpoint curve definition file.
- LimitPointCycle
  Here are all files stored needed to do a fold bifurcation of limit cycles continuation. This includes the initializers and limitpoint of cycles curve definition files.
- MultiLinearForms
  Here are files stored needed to compute high-order derivatives of systems and normal-form coefficients of bifurcations.
- NeimarkSacker
  Here are all files stored needed to do a torus bifurcation of limit cycles continuation. This includes the initializers and torus curve definition files.
- PeriodDoubling
  Here are all files stored needed to do a period doubling bifurcation continuation. This includes the initializers and perioddoubling curve definition files.
- SBML
  This directory contains the routines that allow to import SBML (Systems Biology Markup Language) systems into MatCont. These routines require an update and/or revision.
- Systems
  Here all system definition files and files related to computed curves are stored, except those odefiles which are hard-stored in the directory Testruns/TestSystems because these are used in the testruns. To avoid confusion, it is not recommended to use the names of the odefiles that are present in Testruns/TestSystems.
- Testruns
  Here are some example testruns stored which can be executed from the MATLAB command line. They can be used to run the examples described in this manual and to test if everything is working correctly. The necessary odefiles are stored in the subdirectory TestSystems.

We note that 12 directories are dedicated to a specific curve type, namely:
`Equilibrium`, `LimitCycle`, `LimitPoint`, `Hopf`,
`LimitPointCycle`, `PeriodDoubling`, `NeimarkSacker`, `BranchPoint`,
`BranchPointCycle`, `Homoclinic`, `Heteroclinic` and `HomoclinicSaddleNode`.

Three other directories, namely `HomotopyHet`, `HomotopySaddle` and `HomotopySaddleNode` are initialization directories to a specific curve type.

The remaining 8 directories are not dedicated to a specific curve type.

The only files which are not in any of these directories are `init.m`, `cpl.m`, `matcont.fig` and `matcont.m`. The function `init` must be called before using the command-line toolbox so that MATLAB can find all the needed functions. `cpl` is used to plot the results of the continuation in CL_MATCONT (for details see §3.9). `matcont.m` is the start-up file of the GUI version MATCONT, and `matcont.fig` is the related figure-file.