The group page allows users to load multiple sequences files (in the Fasta, Nexus, Pir, Phylip, Stockholm or Clustal format) and manually organize individual sequences in groups. Don't forget to align your sequences before loading them into SimPlot++. For each of the groups created by the user, a consensus sequence will be generated by SimPlot++. The % threshold for consensus sequences can be modified in the preference tab of the menu. The consensus groups are essential for the SimPlot, BootScan and Network Similarity analyses. The groups can be saved in a Nexus file to avoid recreating them every time.

1. Select your aligned sequence file (DNA or AA) in an accepted format (Fasta, Nexus, Pir, Phylip, Stockholm or Clustal) through the File browser button.
2. Once the file is loaded, the sequence IDs will appear in the Ungrouped Sequences section, on the bottom right.
3. Groups can be created and deleted, and sequence IDs can be moved from the Ungrouped Sequences section to the Group section.
   • Groups can be renamed by clicking on their names.
   • Group colors can be modified by clicking on the corresponding colored circles.
   • A group that has no sequences will prevent the user from running most of the available analyses.
   • A minimum of two groups containing at least 1 sequence each are necessary to run an analysis.
4. Once your groups are created, customized, and are ready to be used, we suggest saving them locally using the Save groups to .Nexus button.
   • This feature will save your initial data in the Nexus format along with the group content, allowing you to skip the group creation process the next time you start SimPlot++.
5. Once these steps are completed, you can run your analysis of choice by selecting it on the top bar of the application.

Below is a summary of the steps presented: