EXPANDS 1.7.1 is now available on CRAN:
https://cran.r-project.org/web/packages/expands
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CHANGES IN EXPANDS VERSION 1.7.1
o Higher subpopulation detection specificity, in particular for small subpopulations. The incidence at which heterozygous and homozygous state of a single subpopulation are falsesly confounded as two distinct subpopulations is reduced.
NEW FEATURES
o 50 simulated samples of various genetic complexities and noise levels included for user testing.
o Whenever possible, SNVs are assigned not only to the subpopulation in which they first occurred, but also to descending subpopulations.
o New phylogeny plotting option: user can choose between consensus and germline population to be included as control.
o New subpopulation plotting options (function plotSPs).
o Two additional output files are created: subpopulation specific ploidy matrix and a summary file of all detected subpopulations, including information on the inferred ancestor and the closest descendant of each subpopulation.
BUG FIXES
o Fixed bug where rare scenarios would lead to wrong subpopulation specific ploidy assignments at specific mutated loci.