trimAl v1.2 has been implemented in the new Phylemon webserver version, 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 analyzes.
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.
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, use one of the examples available or paste your input alignment.
Once the raw alignment is uploaded, firstly, you need to decide if you want to remove spurious sequences from your alignment as a previous step before trimming your poor aligned residues. Secondly, you need to select among the different trimming options, there are these automated methods:
Also, you can find these options among the available ones:
If you use the user-defined 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.
Along this wiki page, you will get more information how all these options work.