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Weekly reading: NGS technology and inference challenges in review

Summary of Weekly Discussion papers read last semester (Fall 2014) on Next-Generation Sequencing methods and related phylogenomic inference challenges. With a few diversions in between. In chronological sequence.

  1. Barker. 2014. Philosophy of statistical phylogenetic methods.
  2. Witteveen. 2014. Naming and contingency: the type method of biological taxonomy.
  3. Lemmon & Lemmon. 2013. High-throughput genomic data in systematics and phylogenetics.
  4. Mardis. 2013. Next-Generation Sequencing platforms.
  5. Bybee et al. 2011. Targeted Amplicon Sequencing.
  6. Lemmon et al. 2012. Anchored Hybrid Enrichment.
  7. Kumar et al. 2012. Statistics and truth in phylogenomics.
  8. Wright & Hillis. 2014. Bayesian analysis outperforms parsimony for morphological data.
  9. Nguyen et al. 2012. Intermittent evolution and robustness of phylogenetic models.
  10. Schwartz et al. 2014. SISRS – Site Identification from Short Read Sequences.
  11. Narechania et al. 2012. RADICAL – Random Addition Concatenation Analysis.
  12. Philippe et al. 2011. Why more sequences are not enough.

We had some fun discussions. Topic for Spring 2015: Phenotype Ontologies.

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