About how to treat Gaps

[yean...@163.com]

Thanks for your working , IQ-TREE is really fast.

I have a problem when I'm doing Ancestral sequence reconstruction , I aligned my CDS sequence by Muscle Codons , and all the sequences can be correctly translated into an amino acid sequence .

But when I get the Ancestral sequence , I found that the Ancestral sequence contains gaps in wrong position caused the sequences can not to be correctly translated into an amino acid sequence . After  I replaced the gaps into A/T/C/G , then the Ancestral sequence can be correctly translated .

I know that IQ-TREE treat GAPS as unknown characters in a similar  way to other ML software  .In my opinion if the sequence is aligned by Codons , the gaps in  Ancestral sequence should also like a Triple codon .

And I know some software like MEGA , can treat gaps in "Use all sites" way,whether IQ-TREE has a similar setting ,sometimes the gaps also have biological significance.

I am wondering if you would like add "Use all sites" into IQ-TREE , thanks for your work again.

[Minh Bui]

Hi there,

I need more information before answering your question. Can you pls paste the command line you used? Did you use DNA or codon models? (e.g. using codon models might be more appropriate here). What is the “Use all sites” option of MEGA doing? What do you mean by “in wrong position”? (Does it mean, that the gaps are not multiple of 3 or are not in the right frameshift?)

Cheers

Minh

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