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https://forum.ugene.net/forum/YaBB.pl General Category >> Feature Requests >> Add a tool for multiple alignment cleaning https://forum.ugene.net/forum/YaBB.pl?num=1565864745 Message started by Mike Shelk on Aug 15^th, 2019 at 5:25pm

Title: Add a tool for multiple alignment cleaning
Post by Mike Shelk on Aug 15^th, 2019 at 5:25pm

There are several programs that can automatically detect poorly aligned regions in a multiple alignment and remove them. For example, Gblocks and TrimAL are popular with 6000 citations and 2000 citations respectively. I and, I think, many other users will be glad if you incorporate one of these tools into UGENE.
Also, thank you for your job. Donated 10 euros today.

Title: Re: Add a tool for multiple alignment cleaning
Post by Olga Golosova on Aug 15^th, 2019 at 6:36pm

Thank you for the feedback! We'll consider integrating these tools.

You've also recently proposed to integrate DESeq2. Do you use it and these two tools for different projects or for the same one? I'd like to understand the analysis workflow in general...

Quote:

Also, thank you for your job. Donated 10 euros today.

Received! Thank you very much!

Title: Re: Add a tool for multiple alignment cleaning
Post by Mike Shelk on Aug 15^th, 2019 at 6:49pm

This is for two different projects. Gblocks is good for an alignment cleaning prior to a phylogenetic tree building. I need it for a phylogenetic study. DESeq2 is for differential expression analysis, which is a part of another project.

Title: Re: Add a tool for multiple alignment cleaning
Post by Olga Golosova on Aug 15^th, 2019 at 6:50pm

Ok, I see, that's what I thought.