Publication-Quality Multiple Sequence Alignment

Question

[l.souza]

Hello everybody,

I run some alignments and I would like to generate great images from the ALN file. What can I use to make publication-quality images, preferably, with extra graphics.

[Pierre Lindenbaum]

see Low Resolution Sequence Alignment Visualization

[l.souza]

Thank you, Pierre! But, does jvarkit show all the aas from the msa or just this bars?

[Pierre Lindenbaum]

just this bar, sorry not suitable for "I mean graphics with the quality, the identity/similarity, etc..." :-)

Answer 1

[l.souza]

I used ESPript 3.0 and JProfileGrid.

Answer 2

[h.mon]

Try BoxShade. What do you mean by "extra graphics"?

edit: see also msa and prettyplot.

[l.souza]

I mean graphics with the quality, the identity/similarity, etc...

[Shicheng Guo]

Anyway to let boxshade to show the result with colorful style? Thanks.