About the MAFFT category

Our first user-contributed software framework: MAFFT ( multiple alignment using fast Fourier transform). Check out our tutorial here.

2 Likes

Hello to everyone!

I am grateful to participate and be part of Galileo contributing to building a better space.

I am a bioinformatician with a great interest in new technologies. MAFFT is widely used in the analysis and comparison of biological sequences in general. I hope it will be useful to all of you.

Any technical or theoretical question I am available to answer!

1 Like

Hey @agustinmpardo! I’m looking forward to working with you to get MAFFT published as a Galileo Mission type. First question I’ll ask is can you point me to a webpage or github link for the MAFFT project?

Hi @todd,
This is the MAFFT official website: https://mafft.cbrc.jp/alignment/software/

@agustinmpardo, in the example you shared with @alex, I believe you used a --thread flag for multithreading. But in the docs for the maftt arguments list, I don’t see that flag as an option. Is that flag documented somewhere else?

Hi @todd,
The documentation you commented is old ( Above says: “This manual does not cover all the features of the latest version (Feb. 2011)”).

Here you can see https://mafft.cbrc.jp/alignment/software/multithreading.html how the “–thread” flag is used.

ah, missed that notice at the top of the page. @alex, did we already get example files from @agustinmpardo for the tutorial that’s going to go up?

@todd,
Yes, I shared with @alex the complete tutorial I created, https://docs.google.com/document/d/1Z_cUOcMz425W3twb-5ivsEulMSv8Dde1IXOSZPPsFYI/edit?usp=sharing to run MAFFT in Galileo. There you can find how to create the necessary files!

Also, you can find the files here: https://github.com/AgustinPardo/galileo_docker_mafft

Great! Thanks @agustinmpardo, the files in the GitHub repository will be very useful.

I’ve almost got MAFTT published as an option in our production configuration wizard, but we’ve got a server-side bug that is holding me up currently. Probably will have to wait until tomorrow to before it gets fixed as people have checked out for the evening. But once it is addressed it will take just a minute to push out and have you try it out.

Great! Where is the Wizard?

Actually I was able to fix it myself. You can check it out now if you log in and create a new Mission.

Great!
But how do you input the fasta file there?

Once you hit submit and create the mission, click on it to bring you to the home page of that Mission. Then you’ll see an “upload file” button.

Click that and it will let you select your .fasta input file from your local machine to upload.

I just tried and it works perfect! Great work!

awesome! and thanks for suggesting that we add MAFFT

@alex told me about the credit as the author in one of the emails some weeks ago. How do you deal with that?

When we post the tutorial, your name will appear as the author like Alex and Matthew do in this one: https://hypernetlabs.io/galileo/tutorials/tutorial-r/

Wonderful. I hope soon!