Custom ladders can be added from plugin version 1.2 onwards. In this version, ladders are stored in a text ﬁle which can be manually edited to add new ladders. This ﬁle can usually be found in the microsatellite plugin installation directory (com.biomatters.plugins.microsatellite.MicrosatellitePlugin), which is usually in the Geneious X.Y data/Plugins folder in your User directory.
Within this directory are a series of sub-directories:
and within this directory is a ladders.txt ﬁle.
This ﬁle contains a tab-separated list of ladders where the ﬁrst ﬁeld is the name of the ladder and the rest are the ladder fragment peak sizes in bp. Geneious must be restarted for changes to this ﬁle to take effect.
If you can't find the microsatellite plugin directory in your data folder try this alternative location:
On a mac: /Library/Application Support/Geneious/plugins/...
On Windows 7: C:/Program Data/Geneious/plugins/... Program Data is a hidden folder so to find it you will have to go to Tools→Folder Options→View and check the "show hidden files, folders and drives" option.