User: su7880

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su78800
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Posts by su7880

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Best tool for Fst calculation with over a thousand SNP among 6 populations??
... Hello, What tools are you guys using to calculate Fst? I tried Arlequin, Genalex etc. They all are good for over all summary. The problem with the software above was that I couldn't have a mean pairwise Fst value between 6 pops for each 1600 SNP loci. Presumably, those 6 pops are composed of two ...
snp written 3.1 years ago by su78800 • updated 3.1 years ago by JstRoRR60
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Answer: A: Is neighbor joining the best approach to look at clustering pattern with populat
... Thank you all. I am sorry what is RF? Can you give me some more details for that? Also, do you know software that might actually take account IUPAC ambiguity codes for phylogenetic inferences? I just saw an argument that MrBayes might or might not use the IUPAC ambiguity codes. Is RAxML a good? ...
written 3.1 years ago by su78800
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Answer: A: Is neighbor joining the best approach to look at clustering pattern with populat
... Thanks for the kind answer. I already tried PCA and various assignments tests like fastStructure, DAPC. However, I still want to look at what NJ does with the data that I have. Any more suggestions? ...
written 3.1 years ago by su78800
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Is neighbor joining the best approach to look at clustering pattern with population genetic data?
... Hello, I am working on a big SNP data set from GBS with over 300 individuals from 34 populations. 34 populations compose three closely related species. I tried various assignment tests to see the pop structure but still wanted to see clustering pattern with different approach. Unfortunately, I ...
snp written 3.1 years ago by su78800
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Comment: C: Linkage disequilibrium in unphased genotypic data
... Hi, Have you tried software "plink"? That worked fine with my data (SNPs from GBS without reference genome). ...
written 3.1 years ago by su78800

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