Bioinformatics Tools For Rad-Seq Data

Question

[Kash]

Hi,

I'm quite new to Bioinformatics. I have some RAD data which I need to align first and then draw phylogenetic trees. Can someone tell me what are the tools I can use?

[Eric Normandeau]

Hi kmkdesilva, There are two questions in your post and the first, it seems, is answered. Please consider removing the part about converting .bcl to FASTA. Look on the forum if there is not already a question covering this and otherwise open a new question with it.

Answer 1

[lelle]

You might want to have a look at Stacks.

[Kash]

Thanks for the suggestion. I'm working on it. But some codes in the manual seems to be not working. Where can I find working codes to install stacks

[Eric Normandeau]

Download Stacks, uncompress the file, from inside the directory, run './configure' then 'make' then 'sudo make install'. This supposes you have Linux or maybe OSX.