Benjamin Hume

4 Questions 4 Answers 0 Followers

Questions related from Benjamin Hume

How are principal components generated directly from eigendecomposition of a 'sample' covariance matrix in PCAngsd?

To generate a PCA from lcWGS SNPs, one may use ANGSD to generate genotype likelihoods and then use these as input to generate a covariance matrix using PCAngsd. The covariance matrix generated...

24 January 2022 4,881 4 View

Is it possible to partition a PERMANOVA results for a given group into variance due to effect and variance due to heterogeneity in dispersion?

Let's say I have a between-sample distance matrix based on genetic similarity and I want to find out if structure in the matrix is correlated/explained by some environmental factors that I have...

05 August 2019 6,482 0 View

How does one get SplitsTree's command line functionality to work?

Hi there, I need a program that can calculate phylogenetic networks. This program must be executable from the command line as I want to implement it into pipelines via python scripting. Looking...

06 October 2018 9,828 2 View

How do I import a large (>200x200) lower-left dissimilarity matrix into SPSS to conduct MDS?

I'm trying to conduct a multidimensional scaling analysis on a dissimilarity matrix using SPSS. I am having no problem importing matrices that are up to 200x200. Over that amount however when...

02 February 2016 6,558 3 View