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.
- Barker. 2014. Philosophy of statistical phylogenetic methods.
- Witteveen. 2014. Naming and contingency: the type method of biological taxonomy.
- Lemmon & Lemmon. 2013. High-throughput genomic data in systematics and phylogenetics.
- Mardis. 2013. Next-Generation Sequencing platforms.
- Bybee et al. 2011. Targeted Amplicon Sequencing.
- Lemmon et al. 2012. Anchored Hybrid Enrichment.
- Kumar et al. 2012. Statistics and truth in phylogenomics.
- Wright & Hillis. 2014. Bayesian analysis outperforms parsimony for morphological data.
- Nguyen et al. 2012. Intermittent evolution and robustness of phylogenetic models.
- Schwartz et al. 2014. SISRS – Site Identification from Short Read Sequences.
- Narechania et al. 2012. RADICAL – Random Addition Concatenation Analysis.
- Philippe et al. 2011. Why more sequences are not enough.
We had some fun discussions. Topic for Spring 2015: Phenotype Ontologies.