Hi,
do you know a tool (server) that colors a sequence alignment file (in FASTA format) by residue type?
Thank you very much
Silvia
I think the best and easy way is Jalview
Using sed
(echo "<body><html><pre>" && curl -s http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/apoex.fa | sed -r -e '/^[^>]/s%([ALVLIFLP])%\1%g' -e 's/^>/\>/' && echo "</pre></body></html>" ) > out.html
If you need it for presentations, papers, etc., there is a very nice LaTeX package: http://www.uni-kiel.de/Pharmazie/chem/Prof_Beitz/pdf/texshade.pdf
Have a look: http://multalin.toulouse.inra.fr/multalin/multalin.html
Colours residue based on different properties and has various output types. It has many other sequence functions too.
Jalview www.jalview.org) has many option for colouring whole alignments or groups. I have added the link to a youtube video about this. Plus there are videos about how to change the appearance of the alignment and exporting journal quality figures.
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version 2.3.6
I am using windows. So, How do I run this command?
You could try Cygwin