Rowan Schley

6 Questions 8 Answers 0 Followers

Questions related from Rowan Schley

Is it possible to infer selection from target capture data?

Has anyone done tests of selection (Dn/Ds, MK etc) on phylogenomic data (specifically, target capture) for many species? The major problem is removing stop codons, since the locus alignments are...

22 May 2023 1,015 2 View

Do any tools exist for profiling phylogenetic informativeness on genome-scale datasets?

In the past I have used PhyDesign (http://phydesign.townsend.yale.edu/) to profile phylogenetic informativeness on smaller phylogenomic datasets, but I was wondering if any new iterations/similar...

14 September 2022 7,950 0 View

How do I plot hybrid triangles of hybrid index and interspecific heterozygosity using RADseq data?

I have tried calculating and plotting these with HiEst, Introgress etc but with no luck. Is there a more modern method to do this, using ddRADseq data?

20 May 2020 527 3 View

What is the best way to date a phylogenomic tree?

What is the best way to date a phylogenomic tree using fossil calibration? It is more or less straightforward with a few Sanger loci using programs like BEAST, but it becomes intractable with...

27 February 2020 4,581 8 View

How do you estimate Fst per-locus and find outliers without BayeScan?

Hi there, I have ddRADseq data, with RAD-loci assembled de-novo using the STACKS pipeline for two species and their hybrids. As such, I was wondering how I could estimate Fst for each of those...

31 October 2018 5,160 4 View

How do I plot the output from Bayesian estimation of genomic clines (bgc)?

Does anyone know how to plot the result outputs (alpha, beta and quantiles) from Bayesian estimation of genomic clines (bgc)? The manual recommends to do so in R, but I am unsure of how to do the...

06 August 2018 4,742 7 View