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How to align 15 different subspecies ?

Hi there,

Im currently struggling to align 15 different subscpecies of a bacteria. I have dowloaded their genomes and annotate them. Now I am suppose to align them but i just dont know how. What are the files and the formats used as an input and is there any missed step i should've have done before aligning? In some, reference sequence is needed hence, what the respective input for it ?

Thank you.

alignment genome sequence gene align
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updated by Jean-Karim Heriche Jean-Karim Heriche • written by sadstudent • sadstudent

2 answers

Have a look at a multiple genome aligner. Mugsy might be a good start.

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written by colindaven colindaven

Have a look at this bacterial comparative genomics tutorial.

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written by Jean-Karim Heriche Jean-Karim Heriche

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