I have a SNP dataset called from 48 individuals across 4 species. 1.8 million SNPs. I am looking for some opinions on the best programs to build a phylogeny of such a large dataset -- these SNPs are unphased.
Hello,
I think you should focus at methods based on summary statistics (ASTRALII, MP-EST) because of the size of your dataset. I can suggest also suggest the new method from Chifman and Kubatko implemented in SVDquartets (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296144/). For a comparison of the performance of summary methods and SVDquartets, you can check this article (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4602346/).
Hope this can help you,
Best,
Hi Ashley,
We used SNAPP (https://www.beast2.org/snapp/) that it is an extension of BEAST. Nevertheless, I think that it could be a problem to handle 1.8M of SNPs. You always could create datasets of ~10K - ~100K random SNPs and create independent trees, reconciling them latter on.
I hope this helps,
Best regards
Aureliano
You should try RaXML:
Stamatakis, A., 2014. Raxml version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics.
Cheers
dlc
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