Hi,
Is there an existing tool that can trim multiple sequences alignement (MSA) in order to get only aligned sequences of the same length?
I am working with sequences from very different lengths (some partial, some complete) and aligned them with Mafft. So I was wondering if a tool on a Galaxy server can do the job and trim all sequences in order to keep only the matching length of these sequences because I want to build a phylogenetic tree with them. I saw that Galaxy presents the ClipKIT tool but I can not find it on global or european servers https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=487edd606fb9b39b&tool_config=%2Fsrv%2Ftoolshed-repos%2Fmain%2F006%2Frepo_6089%2Fclipkit.xml&changeset_revision=770695339600&render_repository_actions_for=tool_shed.
I saw on some blogs that trimAL could also do the job but it is not on your servers from what I saw. Do you have similar tools ?
Thanks in advance
The repository you found is a bit interesting. The development repository linked back to the original tool repository, not to a Galaxy wrapper repository. It is a Bioconda package – and has a wrapper with test data and and other things we usually look for, so that is all perfect for a Galaxy wrapper. Once actually ready, it could certainly be considered for the UseGalaxy servers unless there is something I am missing…
So, I have lots of questions! Is it ready for general use? Are they still testing it out? Do they host it at some server that is not generally known? Where is the development repository? I would suggest opening an issue ticket at their site asking them what the status is. I searched the repository that is linked with “galaxy” and didn’t find anything but may have missed it!
Meanwhile, what about an alternative? This tool will consume the multiple sequence alignment data in (gapped) fasta format directly. There are tutorials linked at the bottom of the form if you would be interested in examples. See → FASTTREE build maximum-likelihood phylogenetic trees
Hope this helps, and please keep us updated if you have time. Post back the issue ticket you open or similar? Thanks! And if anyone else has more information about this tool, please feel free to correct or update here! 