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mikolmogorov / maf2synteny

A tool for recovering synteny blocks from multiple alignment
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How to set the reference genome #12

Open kiwijiji opened 6 months ago

kiwijiji commented 6 months ago

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 commented 6 months ago

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