CherryML: scalable maximum likelihood estimation of phylogenetic models

Author:

Prillo Sebastian,Deng Yun,Boyeau Pierre,Li Xingyu,Chen Po-Yen,Song Yun S.ORCID

Funder

U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences

Publisher

Springer Science and Business Media LLC

Subject

Cell Biology,Molecular Biology,Biochemistry,Biotechnology

Reference28 articles.

1. Dayhoff, M. O. & Schwartz, R. M. A model of evolutionary changes in protein. In Atlas of Protein Sequence and Structure, Ch. 22, 345–352 (National Biomedical Research Foundation, 1978).

2. Jones, D. T., Taylor, W. R. & Thornton, J. M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8, 275–282 (1992).

3. Whelan, S. & Goldman, N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18, 691–699 (2001).

4. Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).

5. Le, S. Q. & Gascuel, O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 25, 1307–1320 (2008).

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