Recent alternative to LalnView

Question

[maxime.policarpo]

Dear everyone,

I was wondering if there were some recent program to visualize the alignment between two genome regions across two or more species. For example I would like to have a representation of two regions with the same genes across two species, with some colored shapes indicating the conserved regions. I know that there is a famous program called LalnView that can do what I want (http://en.bio-soft.net/format/Lalnview.html) but I was wondering is there were more recent alternatives and for a set of 10 species ?

Thanks a lot for any help provided,

Best,

Maxime

Answer 1

[maxime.policarpo]

Thank for your answers. After checking your propositions, I don't think there are very good alternatives, as annotations must come from genbank files while I only have custom annotation files.

After many searches, I have found a R package that could suit my need : genoPlotR (https://genoplotr.r-forge.r-project.org/pdfs/genoPlotR.pdf).

Thanks again and have a good day,

Maxime

[maxime.policarpo]

Even better R package to my opinion : gggenome :)

Answer 2

[Michael]

MAUVE is quite user-friendly. I normally run it on the Linux server and have a X11 user-interface locally.

Here is a video tutorial on youtube:

Answer 3

[Joe]

SibeliaX and clinker are great for doing whole genome and genome region comparisons.