Multi-sequence alignment visualization

Question

[Gregor Rot]

Dear all, what would be the visualization tool to use to visualize multi-sequence alignment (for now 4 sequences, 20kb), perhaps with structural differences and gene annotation on top? Does something like this exist, at least to help build an initial version that can be then edited in Illustrator or some other vector editing software? Thanks for all the suggestions, Gregor

[cmdcolin]

I collect many types of genome visualization tools including MSA, some here. Could browse to see what fits your needs but if you need interactive probably jalview is one of the best options. https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=MSA

Answer 1

[Gregor Rot]

Clustal on EBI is suggesting Jalview, http://dx.doi.org/10.1093/bioinformatics/btp033

Any other alternatives? Can't seem to run it on Mac :)

[patrickdm]

Can't seem to run it on Mac :)

I think it does.

http://www.jalview.org/getdown/release/

Jalview executable .jar file

This requires existing Java installation and can be launched via java -jar jalview-all-2.11.1.7-j1.8.jar

or install via Conda

A Jalview conda package is also available (tested on OSX and Linux) thanks to the great folk over at BioConda

hth

[Gregor Rot]

Yep will have to do some command line (java -jar...), since installing Java and running doesn't seem to work on my Mac, thanks!

[Gregor Rot]

Jalview from bioconda: https://anaconda.org/bioconda/jalview

conda install -c bioconda jalview

[Michael]

Jalview is Java, it runs fine on Mac.

Answer 2

[Gregor Rot]

Jalview on Mac seems to be very shaky / looks clumsy? Well probably like most of the JAVA GUIs...

[Michael]

Yes, like any other Java app on MacOS it looks clumsy but I don't bother, because it's free and gets the job done. There are other tools like Geneious, but they cost $$. You should update Jalview to 2.11.1.7.

There are also TeX and R packages (texshade and msaPrettyPrint).

[Gregor Rot]

thanks, ok will update, this was downloaded and installed by bioconda