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I would like to make an evolutionary tree using the SNP data from DArTseq. Are there any software or packages available for this purpose? I came across the software SNphylo, but its home page is not updated. Your suggestions would be appreciated.

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    $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Commented May 22, 2023 at 7:04
  • $\begingroup$ Welcome @Lama You would need to explain DArTseq and the data set size $\endgroup$
    – M__
    Commented May 22, 2023 at 7:12

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At present I would simply use iqtree

iqtree -s file -m GTR+I+G -T 6 -B 1000 

This will parallelise across 6 CPUs and results in 1000 bootstraps, whilst GTR is the mutation model, which models invariant sites under a 4 category gamma distribution. This is a robust model.

You can view the tree in FigTree.

The DNA file is in fasta format

> seq1
AGACGT
>seq2
AGAAAT

If there's an 'unknown' format bug let me know because I only work in data pipeline so I forget if I've shifted the format.

The result will be in the treefile and is a professional quality tree, complete with bootstraps.

The I parameter here could omitted for this dataset because I assume all none of the sites are invariant.

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  • $\begingroup$ @M_ Thank you for you answer. DArTseq is one of the cheap and easy but efficient genotyping-by-sequencing platforms which allow genome-wide marker discovery through restriction enzyme-mediated genome complexity reduction and sequencing of the restriction fragments (Edet et.al. 2018). I am attempting to construct a phylogenetic tree using the results of DArTseq rather than the FASTA sequences. $\endgroup$
    – Lama
    Commented May 24, 2023 at 0:35
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    $\begingroup$ @Lama its a simple format shift. Maybe conversion of DArTseq to fasta is a good question to raise? At the end of the day the theory is universal if the output is nucleotide data. We'd need to see the new type first, but it's likely very easy. You can build trees from anything and everything - its the underlying theory that counts. $\endgroup$
    – M__
    Commented May 24, 2023 at 0:52

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