For your convenience alignment with variable sites printed to file.phy

[John jiang]

Hi Developers:

    I encounter one question. My data is SNPs, then I concatenated them into fasta file format based on the genotype, then I run the iqtree with command:

    iqtree -s file.fasta -m GTR+G+ASC -b 100 -nt 10 -st DNA

    But I got one error: 

ERROR: For your convenience alignment with variable sites printed to file.fasta.varsites.phy

ERROR: Invalid use of +ASC because of 912724 invariant sites in the alignment

I am not sure the reason, So can you help this?

And the next I run the iqtree with the file.fasta.varsites.phy, is this right?

Any help will be appreciated!

[Minh Bui]

Hi John,

Please first have a look at this FAQ: http://www.iqtree.org/doc/Frequently-Asked-Questions#why-does-iq-tree-complain-about-the-use-of-asc-model

How many sites are you left with, if these nearly 1M sites are removed?

I believe for SNP data, character R is interpreted as "A and G”, and not “A or G” (see the above section of the FAQ). That’s why the warning about too many invariant sites. Therefore, using a standard DNA substitution model might not be appropriate. 

Alternatively, you can use the “polymorphism aware" model. Please look at the document as well. And some previous discussions here about the PoMo model.

Cheers,

Minh

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