data requirements

[Ollie White]

Hello,

Am I right in assuming that this software is not applicable to reduced representation sequencing approaches such as RAD-seq or Genotyping By Sequencing, because it is not possible to construct individual gene trees? 

Cheers

Ollie

[Cécile Ané]

yes, this is correct  --unless you have a genome map that could help you build loci made of multiple markers next to each other on the genome.

[Ваня Двояшов]

Hi, I also have the quaddRAD seq data and reference genome. I used ref_map.pl script in stacks to get the list of loci, so I'm able to concatenate nearby ones. I choose the distance in 10,000 bp between two loci to concatenate, is this an adequate choice? (My species diverged about 0.5 mya). Also, can I assume that if I accidentally concatenate two loci with different topologies, I won't have missed any information because the inconsistency will be reflected in the mbsum file for this big new locus?

Cheers

Ivan