> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/trajectory-analysis.md).

# Trajectory Analysis

Cells undergo changes to transition from one state to another as part of development, disease, and throughout life. Because these changes can be gradual, trajectory analysis attempts to describe progress through a biological process as a position along a path. Because biological processes are often complex, trajectory analysis builds branching trajectories where different paths can be chosen at different points along the trajectory. The progress of a cell along a trajectory from the starting point or root, can be quantified as a numeric value, pseudotime.

Partek Flow offers Monocle 2 and Monocle 3 methods.

* [Trajectory Analysis (Monocle 2)](/partek/partek-flow/user-manual/task-menu/trajectory-analysis/trajectory-analysis-monocle-2.md)
* [Trajectory Analysis (Monocle 3)](/partek/partek-flow/user-manual/task-menu/trajectory-analysis/trajectory-analysis-monocle-3.md)

## Difference Between Monocle 3 and Monocle 2

Major updates in Monocle 3 (compared to Monocle 2) include:

* Monocle 3 learns the principal trajectory graph in the UMAP space;
* the principal graph is smoothened and small branches are excluded;
* support for principal graphs with loops and convergence points;
* support for multiple root nodes.

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.


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