Alternative free software for recombination rate estimation ?

Hi all,

I have a simple radseq data: parents and multiples offsprings. I used Stacks to call SNPs and I am looking to estimate recombination rate in different regions of my genome.

I found Joinmap (https://www.kyazma.nl/index.php/JoinMap/) but apparently you need a licence for this.

I would like to know if you have any recommendations for free (and/or open source) software to estimate recombination rate from a .vcf file ?

Thanks for your help.

radseq joinmap stacks

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written 5.3 years ago by Picasa

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