A general comparison of relaxed molecular clock models.

No abstract is available for this paper.

• Publication year

  2007

• Venue

  Molecular biology and evolution

• Publication date

  2007-12-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1093/MOLBEV/MSM193PMID 17890241
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• BMC Evolutionary Biology BioMed Central Research article

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  2006influential reference
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  2005cited by this paper
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