Quartet MaxCut not available; alternative species tree methods

[alexfranzen]

Hi all. I was wondering if there is an alternative for constructing a species tree from BUCKy output because it appears the link for Quartet MaxCut is broken or doesn't exist anymore? I've scoured the internet and can't seem to find a downloadable file anywhere and not sure if this occurred recently. I'm working with "3RAD" RADseq data and using ipyrad to process data. Would generating a species tree using tetrad (https://ipyrad.readthedocs.io/en/master/API-analysis/cookbook-tetrad.html ) from the same dataset/taxon set be a reasonable substitute? It seems like the starting species tree is really only needed to optimize the SNaQ analysis. The alternative pipeline of RAxML/IQ-TREE and ASTRAL still works, but it seems like using MrBayes and BUCKy is how the documentation is primarily organized and might provide a more "robust" result. Thanks in advance for the advice!

[cecileane]

I don't have time to help with finding Quartet MaxCut. There could be many substitutes to the Quartet MaxCut piece of the pipeline: perhaps weighted Quartet MaxCut (newer, so perhaps still available & maintained), or TREE-QMC or others.

But stepping back, that is not necessary for downstream analysis with PhyloNetworks. I didn't understand what you wanted to substitute: if it was the whole BUCKy pipeline (on all subsets of 4 taxa).

1. To get a good starting tree, ASTRAL or some other estimation of a species tree would be just fine.
2. To get estimates of quartet concordance factors, BUCKy is just the best at doing so while accounting for gene tree error / gene tree uncertainty in a principled way. The output is not a species tree: it's a table listing all subsets of 4 taxa, and multiple columns for each, including 3 columns for the proportion of genes having each of the 3 splits. There is no need to use Quartet MaxCut to get that table. Running Quartet MaxCut after BUCKy can safely be removed.

[crsl4]

Yes, I am trying to replace Quartet MaxCut for TREE-QMC. I attach the Quartet MaxCut version that I have (and that the authors have authorized me to share when I teach the TICR pipeline), but I agree with Cecile's point in that it is not really needed.

QMCN.tar.gz

[alexfranzen]

Hi Claudia and Cécile, thanks for the helpful answer and for maintaining the PhyloNetworks resource. You certainly answered my question. It seems like Quartet MaxCut is really for convenience since that's what the get-pop-tree.pl script uses. I have been able to obtain the CF table from BUCKy without any problems and just wanted to make sure using an independently generated species tree in combination with the CF table as input to SNaQ was ok. I've been able to generate a species tree with a different method, so I'll proceed with the analysis. The only time I've run SNaQ was at the MOLE workshop back in 2023 and was trying to follow my notes from the computer lab as close as I could. So I guess I was being a little too strict with my interpretation of the pipeline. Thank you again and take care, Alex Alex Franzen (He/Him/His) Ecology and Evolutionary Biology Graduate Program Vaughn Lab Oklahoma Biological Survey

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________________________________ From: Claudia Solis-Lemus ***@***.***> Sent: Sunday, February 2, 2025 2:17 PM To: JuliaPhylo/PhyloNetworks.jl ***@***.***> Cc: Franzen, Alex ***@***.***>; Author ***@***.***> Subject: Re: [JuliaPhylo/PhyloNetworks.jl] Quartet MaxCut not available; alternative species tree methods (Issue #224) Yes, I am trying to replace Quartet MaxCut for TREE-QMC. I attach the Quartet MaxCut version that I have (and that the authors have authorized me to share when I teach the TICR pipeline), but I agree with Cecile's point in that it is not really needed. QMCN.tar.gz<https://urldefense.com/v3/__https://github.com/user-attachments/files/18633746/QMCN.tar.gz__;!!GNU8KkXDZlD12Q!5wE4D5u1IXZ7GrujNVa1RF8TPu2ofhEkKvv3aVkJv1PNWVB6dCg07C4fyWuEYm2x10X9h4CayEeAXUASzDeEdJur$> — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/JuliaPhylo/PhyloNetworks.jl/issues/224*issuecomment-2629539512__;Iw!!GNU8KkXDZlD12Q!5wE4D5u1IXZ7GrujNVa1RF8TPu2ofhEkKvv3aVkJv1PNWVB6dCg07C4fyWuEYm2x10X9h4CayEeAXUASzHxL1iYM$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/A2HSSPEFZDPWADH6DB7BSXD2NZ4MRAVCNFSM6AAAAABWIMJKXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMRZGUZTSNJRGI__;!!GNU8KkXDZlD12Q!5wE4D5u1IXZ7GrujNVa1RF8TPu2ofhEkKvv3aVkJv1PNWVB6dCg07C4fyWuEYm2x10X9h4CayEeAXUASzFD4mgJ9$>. You are receiving this because you authored the thread.Message ID: ***@***.***>