Use of the webserver interface
trimAl v1.1 has been implemented in the Phylemon webserver, an online platform for phylogenetic and evolutionary analyses of molecular sequence data. The TrimAl webserver included in Phylemon provides a user friendly interface and the opportunity to concatenate your trimmed alignment to many different phylogenetic analyses.
You can open an account in Phylemon, this will allow you to store your data for future sessions.
If you do not want to open a user account, just log in as an anonymous user.
Once logged in, you can start by uploading the alignment to be trimmed by using the “select file from your machine” option, this will open a file browser on your computer. Alternatively you can select one alignment from a previous phylemon session or use one of the examples available.
Once the raw alignment is uploaded, you need to select one trimming algorithm, there are three automatic modes:
And one in which you can choose your own parameters:
If you use this last option you would need to specify either a gap or a similarity threshold and, only if you want these options, a minimum coverage threshold and a window size.
At the Getting started section, you will get more information how all these options work.