Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction
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Title
Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction
Authors
Keywords
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Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 34, Issue 12, Pages 3279-3291
Publisher
Oxford University Press (OUP)
Online
2017-10-04
DOI
10.1093/molbev/msx261
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- (2016) Bo Xu et al. GENETICS
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