Circos - genome alignment

Question

[glady]

I am trying to use Circos in Windows for genome alignment, I have downloaded the software and extracted the files from the tar folder. But I am facing some problems in using Circos. 1) How can check whether circos is installed in my system? 2) How can I run the circos scripts?

[5heikki]

Circos is for data visualization, not genome alignment ;)

[glady]

Then which tool, I can use for genome alignment ?

[5heikki]

MUMmer is good given relatively similar genomes.

[glady]

n what about MAUVE ?

Answer 1

[Ibrahim Tanyalcin]

Dear glady,

First check if you have perl installed, on the cmd write:

perl -v

It should print out the version of perl together with some other things. Circos will operate on files with .conf extension which in turn recruits other files. You run circos (which is inside the bin folder of the circos you installed) on this .conf file. Since you are on windows you will need to tell with what to use circos script with. To run circos write:

CWD:\>perl C:\Strawberry\circos-0.67-7\bin\circos -conf path\to\your\myConfig.conf

To check if some modules are missing:

CWD:\>perl C:\Strawberry\circos-0.67-7\bin\circos -modules

There are never versions of circos (v0.69+) which might not need the -conf flag. Verify this from the circos's website.

Hope it helps, Good luck,

Answer 2

[Md]

I have a mauve output, can any body suggest how to use this mauve outputin circos