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cran / MSCquartets

:exclamation: This is a read-only mirror of the CRAN R package repository. MSCquartets — Analyzing Gene Tree Quartets under the Multi-Species Coalescent
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Dear Rhodes, how can I interpret the results of MSCquartets #1

Open lychen83 opened 2 months ago

lychen83 commented 2 months ago

Dear Rhodes,

I have used the quartetTreeTestInd model and plotted the results using quartetTestPlot. However, I don't know how to explain the results. Some papers interpreted the results as: 'When ILS is present, symbols may lie in closer proximity to the centroid indicating substantial ILS or closer to the vertex indicating little ILS. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9016594/' 'Symbols in closer proximity to the centroid suggest ILS, whereas symbols closer to the vertex indicate other mechanisms (such as introgression, phylogenetic inference error, or gene duplication or loss) explaining discordance. https://www.sciencedirect.com/science/article/pii/S1055790324000460' 'Blue circles lying closer proximity to the centroid represent substantial ILS, while closer to the vertex represent little ILS and indicating processes other than ILS should be responsible for the discordance. https://www.sciencedirect.com/science/article/pii/S1055790324000460?via%3Dihub'

However, all these papers did not cite any references. I did not find a similar interpretation in the manual of MSCquartets or the MSCquartets paper: https://doi.org/10.1093/bioinformatics/btaa868. Therefore, I am not sure if these interpretations are correct. In addition, can MSCquartets separate hybridization from other factors such as ILS and introgression?

Thanks a lot for your help.

Best, mscquartets plot

Lingyun Chen China Pharmaceutical University

gaborcsardi commented 2 months ago

Hi, this is a read only mirror of CRAN, please see the package authors in the DESCRIPTION file. Look for Maintainer, BugReports and URL. Thanks!