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CEGA-v1.2

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@ChenHuaLab ChenHuaLab released this 18 Oct 17:44
· 10 commits to main since this release
1.2
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Learn about vigilant mode.

CEGA: a method for inferring natural selection by comparative population genomic analysis across species.

We developed maximum likelihood method for detecting positive selection or balancing selection using multilocus or genomic polymorphism and divergence data from two species. The method is especially useful for investigating natural selection in noncoding regions.

Main changes compared with CEGA v1.1:
(1) CEGA v1.2 adds the option -LRT for implementing the likelihood ratio test as an alternative to the significant test (set -LRT 1 for CEGA-LRT).
(2) The running speed of CEGA v1.2 is improved.
(3) The lower bound of λ is changed from 10^-6 to 10^-4. The upper bound of divergence time T is changed from 10^6 to 10^7.
(4) The normalization of λ is changed.

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