I have my DDRAD sequences aligned in a fasta file. I have 12 populations for 1 species. The sequences in the file look like this:
>CLocus_10732_Sample_342_Locus_1179_Allele_0 [CI_B18.all]
--------------------------------------------------------------------------------
-------------TG-C---AG-------GAGCG-------G--C-----------------------------------
--------------------------GGC----T----------------------------------------------
--CGC-----CGAGC---AG---------CCG---GTGA-C-GCTCG--------------------------------A
-----------------GGAA-----CT----------GTC-G-----------------------------G---G---
----------------C--C-AC--------T-A-C-----AA-AGTGAG-------CC-GCGA-G-C------------
----------------------G---------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-------------------
Looking at other papers using DDRAD the methods mention a step where loci are concatenated, but the methods never mention how this is done. I would like to know how this is done.
I supposed you need to concatenate the sequences first then do the alignment. To concatenate the loci you can used perl script if to do so or you can use FasConcat-G software. And for the alignment you can aligned separately under linux using MAFFT. All alignments that were performed can be visualized using Mesquite sotware.
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