a number of new publications!

It has been a bit since our last update but just added a bunch of new papers to the publications page. This includes a first author publication by graduate student Joseph Walker! Congrats!
Here is the list for the year so far

  • Smith, S. A. and J. W. Brown. accepted. Constructing a comprehensive seed plant phylogeny.
    American Journal of Botany
  • Pease J.B., J. W. Brown, J. F. Walker, C. E. Hinchliff, S. A. Smith. in press. Quartet Sampling distinguishes lack of support from conflicting support in the plant tree of life. American Journal of Botany
  • Fleischmann, A., J. Schlauer, T. Givnish, and S. A. Smith. In press. Evolution of carnivory in angiosperms. Chapter 3. in forthcoming book on Carnivory in angiosperms.
  • Lopez-Nieves, S., Y. Yang, T. Feng, S. A. Smith, S. F. Brockington, and H. A. Maeda. In press. Relaxation of Tyrosine Pathway Regulation Underlies the Evolution of Betalain Pigmentation in Caryophyllales. New Phytologist
  • Brown, J. W., N. Wang, and S. A. Smith. 2017. The development of scientific consensus: analyzing conflict and concordance among Avian phylogenies. Molecular Phylogenetics and Evolution https://doi.org/10.1101/123034
  • Brown, J. W. and S. A. Smith. 2017. The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates. Systematic Biology https://doi.org/10.1101/113720
  • Walker, J., Y. Yang, M. Moore, S. F. Brockington, and S. A. Smith. 2017. Conflict among carnivores: whole transcriptomes unable to resolve the carnivorous clade of Caryophyllales. American Journal of Botany. https://doi.org/10.1101/115741
  • Smith, S. A., M. J. Moore, S. F. Brockington, and Y. Yang. 2017. Disparity, Diversity, and Duplications in Caryophyllales. New Phytologist. https://doi.org/10.1101/132878
  • Yang, Y., M. J. Moore, S. F. Brockington, J. Mikenas, and S. A. Smith. 2017. Improved transcriptome sampling pinpoints widespread paleopolyploidy events in Caryophyllales New Phytologist. https://doi.org/10.1101/143529
  • Brown, J., J. Walker, and S. A. Smith. 2017. phyx: Phylogenetic tools for Unix. Bioinfor- matics. https://doi.org/10.1093/bioinformatics/btx063
  • Yang, Y., M. J. Moore, S. F. Brockington, A. Timoneda-Monfort, T. Feng, H. E. Marx, Joseph F. Walker, and S. A. Smith. 2017. An efficient field and laboratory workflow for plant phylotranscriptomic projects. Applications in Plant Sciences. https://doi.org/10.1101/ 079582

Phyloseminar notes

Giving the phyloseminar today.
Here are some instructions for the phylo seminar demos
get input files from here
http://blackrim.org/datafiles/phylo_seminar_files2014.tar.gz

get taxonomy from here
http://files.opentreeoflife.org/ott/

git clone https://github.com/OpenTreeOfLife/treemachine.git
git clone https://github.com/OpenTreeOfLife/gcmdr.git
git clone https://blackrim@bitbucket.org/blackrim/avatol_nexsons.git

cd ../treemachine
./mvn_cmdline.sh

#DEMO 1 -- atol trees
cd treemachine
java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar justtrees atol/RAxML_bootstrap.WITH_MT_BS100.rr T life atol.db
java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar graphml life atol.graphml F atol.db

#DEMO 2 -- tree + taxonomy
cd ../gcmdr
edit config file (the demo one is called stephen_laptop_conf.py)
edit load_taxonomy.py and synth_one_study.py to import your conf file
python load_taxonomy.py
python synth_one_study.py

#DEMO 3 -- birds
cd ../treemachine
bash DEMO_run_birds_example.sh

#DEMO 4
web site here http://files.opentreeoflife.org/