trimAl_use_inputfiel

usegalaxy.eu support
,
1

I want to know if there are any special requirements for trimAL input files? For example, amino acid alignment files. Amino acid files are used to ensure that the ambiguous regions are deleted three by three.

Or is it enough to just input the nucleotide alignment results, such as the COI nucleotide alignment file after MAFFT?

2

Hi @yaoyuan

Is this the tool you are using?

  • trimAl for automated alignment trimming(Galaxy Version 1.5.0+galaxy1) (link at EU)

If yes, then you are correct: the tool is expecting a file with multiple protein sequences in one of the supported multiple formats. This tutorial has a short example → https://training.galaxyproject.org/topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html#alignment-trimming

And, I was able to confirm that the version loading from the tool panel has a small bug.

What to do:

  1. Load the tool form
  2. Navigate to the earlier version of the tool → trimAl for automated alignment trimming(Galaxy Version 1.5+galaxy0) and use this instead
  3. How to navigate tool versions → FAQ: Changing the tool version

If that is not enough to resolve your issue, do you want to share the example? How to share your work is in the banner of this forum. You might be able to share just screenshots for this: capture the URL of the browser window and the top of the tool form so we can see those details. You can also capture what your input file looks like now and any error messages you are getting from the tool. Where to find all of this is in this guide → How to get faster help with your question

Let’s start there, thanks for asking the question! I’m guessing that your data had produced an error and were not able to resolve it, but please clarify and we can follow up more. :slight_smile: