what happens to sites not specified in a partition file?

[John Soghigian]

hello all,

Let's say I have a partition file that is specifying 1st and 2nd codon positions in the alignment, but not the third position, e.g.:

DNA, og1 = 1-500\3

DNA, og1_2 = 2-500\3

DNA, og2 = 501-900\3

etc...

the full alignment still contains the entire alignment in frame, so it still has 3rd positions. Does IQtree ignore any columns not specified in the partition file for ML inference?

[Minh Bui]

Hi John,

The simple answer is Yes, IQ-TREE will ignore all positions not included in the partition file.

Cheers

Minh

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