.fas or .fasta to .axt for KaKs Calculator

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2.2 years ago

JM • 0

How do I convert a .fas or .fasta file into .axt?

I tried to run the .fas/.fasta file of my aligned sequences that I edited thru BioEdit. But the Ka/Ks value results in N/A and now I'm stuck.

Example .fas file: enter image description here

axt KaKs fasta • 1.7k views

ADD COMMENT • link updated 2.2 years ago by Ram 45k • written 2.2 years ago by JM • 0

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Past thread that may be useful:

Fasta to axt - KaKs Calculator

ADD REPLY • link 2.2 years ago by GenoMax 154k

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I saw this thread but unfortunately I'm not familiar with Python(?).

ADD REPLY • link 2.2 years ago by JM • 0

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If you have an aligned fasta file as shown in the example in thread linked above you can use the commands shown in the thread. No programming needed. Replace your file name in place of example-file.fasta or file.fa depending on the answer you use.

ADD REPLY • link 2.2 years ago by GenoMax 154k

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It gave an error: "^ invalid char ''' in expression". I tried to fix it it but errors just keep on appearing.

ADD REPLY • link 2.2 years ago by JM • 0

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Can you show output of head -5 your_aligned.fa?

ADD REPLY • link 2.2 years ago by GenoMax 154k

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This is my .fas file: enter image description here

ADD REPLY • link 2.2 years ago by JM • 0

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