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Posts tagged ‘phylogenomics’

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.

Weekly reading: Why more sequences are not enough

Momentarily the last item in our semester-long NGS and phylogenomic analyses reading sequence. Phenomics (and ontologies) will be on the continuing menu, soon enough.

Philippe, H., H. Brinkmann, D.V. Lavrov, D.T.J. Littlewood, M. Manuel, G. Wörheide & D. Baurain. 2011. Resolving difficult phylogenetic questions: Why more sequences are not enough. PLoS Biology 9(3): e1000602. Available on-line here.

Weekly reading: RADICAL – Random Addition Concatenation Analysis

An interesting paper and powerful tool that cuts empirically through the longstanding and somewhat dispiriting total evidence ‘versus’ partitions discussion thread in our field.

Narechania, A., R.H. Baker, R. Sit, S.O. Kolokotronis, R. DeSalle & P.J. Planet. 2012. Random Addition Concatenation Analysis: A novel approach to the exploration of phylogenomic signal reveals strong agreement between core and shell genomic partitions in the Cyanobacteria. Genome Biology and Evolution 4(1): 30-43. Available on-line here.

Weekly reading: SISRS – Site Identification from Short Read Sequences

This week’s discussion will focus on a novel method to identify and separate signal from noise for Next-Generation sequencing datasets – SISRS.

Schwartz, R.S., K. Harkins, A.C. Stone & R.A. Cartwright. 2014. A composite genome approach to identify phylogenetically informative data from Next-Generation Sequencing.

Weekly reading: Anchored Hybrid Enrichment

Another, ground laying paper for us to read and discuss this week on one of the most potent new NGS approaches: Anchored Hybrid Enrichment.

Lemmon, A.R., S.A. Emme & E.M. Lemmon. 2012. Anchored Hybrid Enrichment for massively high-throughput phylogenomics. Systematic Biology 61: 727–744. Available on-line here.

Weekly reading: Bybee et al. on Targeted Amplicon Sequencing

Next up in the weekly Massive, Parallel Sequencing discussion series is:

Bybee et al. 2011. Targeted Amplicon Sequencing (TAS): a scalable Next-Gen approach to multilocus, multitaxa phylogenetics. Genome Biology and Evolution 2011, 3: 1312–1323. Available on-line here.