Software to calculate expected sequence identity between two species, given speciation time

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9.1 years ago

Biomonika (Noolean) 3.2k

I have two species, let's say one of them is human and second is one of the species of monkeys. If I align the homologous sequences between these two species, what's the expected sequence identity (given that I know speciation time as well as expected mutation rate)? Is there any software that would do this calculation for me?

I want to do this to verify that my alignments look reasonable.

identity speciation sequence alignment • 2.1k views

ADD COMMENT • link updated 2.2 years ago by Ram 44k • written 9.1 years ago by Biomonika (Noolean) 3.2k

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Do you want to perform this calculation genome-wide, or just for certain genes? Mutation rates vary widely throughout the genome.

Do you have reason to suspect your alignment is fishy? I would do a "poor's man" test, checking if annotated features (coding regions particularly) show good agreement.

ADD REPLY • link 9.1 years ago by h.mon 35k

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