how to use Ka/Ks calculator

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4.5 years ago

drragill ▴ 10

Hi, I want to calculate the divergence time of genes. Can somebody guide me on how to use the KaKs calculator software? Many thanks!

rna-seq alignment gene • 1.6k views

ADD COMMENT • link updated 4.5 years ago by Biostar 20 • written 4.5 years ago by drragill ▴ 10

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Please read the tool documentation, follow it accordingly, and then, if you encounter problems, post a question here. In the question, be as detailed as possible, for example, including a link to the tools page, and try to include sample data to reproduce the error.

ADD REPLY • link 4.5 years ago by h.mon 35k

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Are you referring to the Ka/Ks calculator found here?

https://kakscalculator.herokuapp.com/

ADD REPLY • link 4.5 years ago by Dave Carlson ★ 1.7k

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Dear h.mon and Dave Carlson,

Many thanks for your kind reply. But I encounter a problem as...Original Sequence has unconventional nucleotides. My input sequence (both) was in fasta format as below...

ATGAAAGGCACGTTATCACCCGCTCTAGGGAACCTCGGATCTCTCCAGGTTTTGTTCATT TCTGGAACCAAGTTCATTGCCGGCTCGATTCCCAACAGCTTCTCTAAGCTAACTAGTCTT ACTCAGCTCGTCCTCGATGATAACTCTCTCCAAGGCAACGTTCCTTCTTGTTTAGGCCAT CTTCCGTTCTTGGAGATTCTTTCATTGGCTGGAAACCGTTTCTCAGGTGTTGTCCCAGCG AGTTTGGGGAGCTTGAGAAGCCTCTCTGTGATGATGTTGGCTCGAAACTCTCTCTCTGGT CCAATCCCAGTGACGTTCAAGAACCTTGTCAAGCTTCAGACTCTTGACCTCAGCTTCAAT ATGTTATCTGGACCGATACCAGACTTCATAGGCCAGTTTCGGAATCTAACAACTCTTGAT CTCTCCAGCAACAGATTCTCCGGGGGACTACCGGTTTCTGTTTACAACTTGGGGAAGCTT

Could you please guide me on which format I should input..in detail. Many thanks!

Sincerely

ADD REPLY • link 4.5 years ago by drragill ▴ 10

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This (these?) sequence is not in fasta format, and I don't see any unconventional characters in it.

ADD REPLY • link 4.5 years ago by h.mon 35k

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