WARNING: 7169 sequences contain more than 50% gaps/ambiguity

[ardy20]

Sorry, I am new to IQ-Tree. I am running IQ-Tree in Conda using a simple default mode but I get the warning for 7169 of my sequences. However, the analysis runs perfectly after the warning. I did the protein alignment in MAFFT to create the input file, including alignment of 106 gene in 65 plant species.

The Warning example (It is only the last lines of warning because there are too many) :

7169 Chenopodium_quinoaXP_021713523.1_L_galactose_dehydrogenase_like 98.12% failed 0.00% WARNING: 7169 sequences contain more than 50% gaps/ambiguity **** TOTAL 97.58% 6977 sequences failed composition chi2 test (p-value<5%; df=19)

Is this an unusual warning and if not, is there any parameter to reduce threshold for the gaps?

[710744562]

Do you know how to solve this problem? I used 270 sequences and 241 sequences failed composition chi2 test (p-value<5%; df=19).

I am looking forward to your reply.

[bqminh]

Hi, there is a FAQ about this here: http://www.iqtree.org/doc/Frequently-Asked-Questions#what-is-the-purpose-of-composition-test

Cheers Minh

On 7 Jun 2023, at 2:49 am, 710744562 @.***> wrote:

Do you know how to solve this problem? I used 270 sequences and 241 sequences failed composition chi2 test (p-value<5%; df=19).

I am looking forward to your reply.

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