Resolving codeml Analysis Issues with Non-Multiples of Three in Sequence Length

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박현선

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Mar 30, 2024, 8:38:09 AMMar 30

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Dear Ziheng Yang,
I hope this message finds you well. I am currently engaged in a comparative genomic study aimed at identifying positively selected genes across multiple genomes. For this purpose, I am utilizing codeml from the PAML package to analyze several single-copy genes.

To enhance the accuracy and reliability of my analysis, I performed pal2nal for codon-based alignment, followed by trimming with Gblocks to refine the alignments. Despite these precautions, I encountered an error when attempting to run the M0 model analysis in codeml. The error indicates that the sequence length in some of the .phy files is not a multiple of three, which I understand is crucial for codon-based analyses.

Given your expertise and experience with codeml, I would greatly appreciate any guidance or suggestions you might have on how to address this issue. Is there a recommended approach to ensure that all sequences are of the appropriate length post-trimming, or any specific advice you could offer for handling such cases in the context of positive selection analysis?

I am eager to resolve this issue promptly and continue with my research. Any help or insights you could provide would be immensely valuable.

Thank you very much for your time and consideration. I look forward to your response.

Best regards,

Hyeonseon Park
Chungnam National University

Sandra AC

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Apr 3, 2024, 10:50:54 AMApr 3

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Hi there,

Thanks for your message! I am not sure what could have gone wrong during the filtering steps that you followed, but you may have to check the output you got from pal2nal and Gblocks to see which sites were filtered out from your sequence alignment. I suspect that something may have gone wrong when you ran Gblocks if you did not specify that your sequence alignment was codon-based, but I may be wrong and something else may have happened.

Hopefully, you can figure out what may have occurred during your bioinformatics filtering procedure. Other PAML users may also have other suggestions!