Recent alternative to LalnView
3
0
Entering edit mode
23 months ago

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

Synteny Evolution Genome Alignment • 1.1k views
ADD COMMENT
1
Entering edit mode
23 months ago

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

ADD COMMENT
0
Entering edit mode

Even better R package to my opinion : gggenome :)

ADD REPLY
0
Entering edit mode
23 months ago
Michael 54k

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:

ADD COMMENT
0
Entering edit mode
23 months ago
Joe 21k

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

ADD COMMENT

Login before adding your answer.

Traffic: 2015 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6