Custom ladders can be added from plugin version 1.2 onwards. Ladders are stored in a text ﬁle which can be manually edited to add new ladders.
Note that Geneious requires the ladder to be in the last dye of your trace. So if you have done a 4 dye run, then your trace should only have 4 dyes and the ladder should be in the last dye. If you have done a 4 dye run but your traces are configured as if 5 dyes are used, then the last dye is likely to be empty so Geneious will not be able to call a ladder.
The ladders.txt 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. If you edit this file then Geneious must be restarted for changes to take effect.
How to find and edit the ladders.txt file
First, ensure you have installed the Microsatellites plugin is installed via menu Tools - Plugins.
Then locate the microsatellite plugin installation directory. The location of this will vary depending on what operating system you are on, and whether Geneious was installed by an administrator - see below for a list of plugin installation locations.
The microsatellite plugin folder is called
Within this folder you will find a series of subfolders:
and within data directory you will find the ladders.txt ﬁle.
Open this file in a text editor and add your ladder, following the format of the other ladders in the file. Then restart Geneious so that it picks up the new information.
Plugin folder locations:
C:\Program Files\Common Files\Geneious\plugins
Note: The Appdata folder is a hidden folder. To find it you will have to go to Folder Options in the Windows Control Panel, and in the View panel and check the option to "show hidden files, folders and drives".
Note the Library folder in Users is hidden on later mac operating systems. To find it you will need to enable hidden files using "command-shift-. (period)".