hapFLK release 1.3
The 1.3 release improves estimation of population trees and kinship matrix.
We are happy to introduce a new version of
hapflk that improves how the population tree is estimated and consequently the estimation of the population kinship matrix.
The improvement concerns mainly situations where no outgroup information is available. In the previous
hapflk versions, in such cases we used a midpoint rooting approach, which could lead to biased estimations of the populations kinship matrix, as exemplified in the recent paper by Gautier (2015). We now implement a maximum likelihood-based approach to (i) identify the branch in the unrooted tree where the root is located and (ii) optimize the root placement within that branch. The rationale is to adjust branch lengths to observed population heterozygosities.
The new implementation makes it possible to use
hapflk in datasets with only two populations and no outgroup information, which was not possible with previous releases. It also corrects a bug with the --keep-outgroup option where the root was previously ill-placed, in particular in datasets with few populations.
All of this has been reimplemented in python, so that performing these procedures with
hapflk no longer requires R nor its packages
- Gautier M. (2015) Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates. Genetics. 10.1534/genetics.115.181453