The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets
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Title
The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets
Authors
Keywords
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Journal
SYSTEMATIC BIOLOGY
Volume -, Issue -, Pages -
Publisher
Oxford University Press (OUP)
Online
2020-01-31
DOI
10.1093/sysbio/syaa008
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- (2019) Gustavo A. Bravo et al. PeerJ
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