Phylogenetic Screening of Ribosomal RNA Gene-Containing Clones in Bacterial Artificial Chromosome (BAC) Libraries from Different Depths in Monterey Bay

No abstract is available for this paper.

• Publication year

  2004

• Venue

  Microbial Ecology

• Publication date

  2004-10-14

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1007/s00248-004-0213-5PMID 15696381
• 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.

• ARB: a software environment for sequence data.

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