Antonis Rokas

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Antonis 08-13-09 200x200.jpg

Duration of Stay

I will be at the workshop from July 23rd till July 26th, 2015.


Institutional home page

http://as.vanderbilt.edu/rokaslab


Lecture Materials

The slides from my lecture can be found here.


Key Papers

Rokas & Abbot (2009) Genomics for evolution

Rokas et al. (2003) Genome-scale evaluation of incongruence

Hittinger et al. (2010) Increasing the genomic depth of the tree of life

Rokas et al. (2005) Limits to resolution

Salichos & Rokas (2013) Overcoming challenges in inferring ancient divergences. Leonidas Salichos was a student in the 2011 course!

Salichos et al. (2014) Novel Measures for Quantifying Phylogenetic Incongruence. Note: the measures described in this paper have been implemented in the latest versions of RAxML, which can be downloaded from here. A draft manual describing how to obtain these metrics can be found here. The RAxML commands required for obtaining these measures are also described in the RAxML manual.

Kobert et al. (2015) Computing internode certainty and related measures from partial gene trees. Note: the measures described in this paper have been implemented in the latest versions of RAxML, which can be downloaded from here.

Other Phylogenomics / Evolutionary Genomics Papers

Soria et al. (2014) Functional Divergence for Every Paralog Patricia Soria was a student in the 2012 course!

Zhou & Rokas (2014) Pathologies of Next-Gen Sequencing Data

Salichos & Rokas (2011) Comparison of Orthology Prediction Algorithms

Rokas & Carroll (2008) Homoplasy in Molecular Data

Ane et al. (2007) Bayesian Concordance Analysis

Rokas & Carroll (2006) Bushes in the Tree of Life


Papers on Evolution of Fungal Metabolism

Slot & Rokas (2011) HGT of toxic gene cluster between fungi

Gibbons et al. (2012) Microbe domestication

McGary et al. (2013) Toxicity drives clustering of metabolic genes in fungi

Wisecaver et al. (2014) Evolution of fungal metabolic pathways Jennifer Wisecaver is a student in the 2015 course!

Lind et al. (2015) Rewiring of fungal secondary metabolic pathways Abigail Lind is a student in the 2015 course!