Likelihood Calculation Felsenstein

[Billyzhang1229]

Likelihood Calculation

This PR introduces a set of functions for computing the likelihood of phylogenetic trees.

Checklist

• Implement the basic version of Felsenstein's likelihood calculation.
• Implement _get_genotype_index to find genotype indices in a mapping array.
• Implement _transition_probability for calculating mutation transition probabilities.
• Implement _calculate_likelihood to compute likelihoods using the transition probabilities.
• Create likelihood_felsenstein as the high-level function orchestrating the likelihood computation.
• Implement a variant vectorised version of likelihood calculation function.
• Implement unit tests for all new functions.
• Add documentation and examples for new functions.

Notes

• The implementation uses Numba parallel=True option in _likelihood_felsenstein.

[coveralls]

Pull Request Test Coverage Report for Build 9000585702

Details

• 113 of 113 (100.0%) changed or added relevant lines in 9 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+1.4%) to 91.202%

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Totals
Change from base Build 8880499253:	1.4%
Covered Lines:	622
Relevant Lines:	682

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💛 - Coveralls

[jeromekelleher]

LGTM, a few minor comments and good to merge.

[Billyzhang1229]

I'm adding one more test to cover all the cases

[jeromekelleher]

OK, ping me when ready for final review