How to set the reference genome

[kiwijiji]

Hi , maf2synteny is a one or multi-reference assisted tool and l noticed that the first sequence always be the backbone in the genomes_permutations.txt file. l wanna ask if there are some parmeters can set the reference or how maf2synteny choose reference ? based on length of genome or something else ?

Thanks a lot !

[mikolmogorov]

Hi,

maf2synteny should follow the order of the genomes from the maf file I think. Are you looking to change the orders of the genomes in the genomes_permutations without any actual change in block structure? There is no parameter to control this, but should be an easy script to write..

Best, Misha