There are several options that you can try that are adapted to thousands of markers.

  + MSTmap (http://138.23.178.42/mstmap/)

  + R/QTL (http://www.rqtl.org/) with instructions to create maps: http://www.rqtl.org/tutorials/geneticmaps.pdf

    Personally I like the last one because it is R so you can play more with the graphs.

   I hope this helps

Hi Marco,

You can use MapDIsto (http://mapdisto.free.fr/) that is Excel-based. It is very easy to use and you do not need any statistical language knowledge (like "R").

Cheers

I like MSTmap (http://alumni.cs.ucr.edu/~yonghui/mstmap.html) which can analyze thousands of markers in a short time. 

Hi Marco,

With this software has been done a lot of maps and genetic works.

http://mapmaker.sharewarejunction.com/

Best wishes

José Manuel Donoso