Supporting Data from Ecological Opportunities and Constraints in the Evolution of Diatoms

<p>2016-02-01<br /> Teofil Nakov</p> <p>Data and code for Nakov, Ruck, Alverson: Ecological opportunities and constraints in the evolution of diatom</p> <p>This packet contains the following files:</p> <p>1. Sequence alignment for 540 diatoms and 2 Bolidomonas: Nakov-etal-542-taxon-alignment-clean.fasta<br /> 2. The constraint topology used in tree searches: Nakov-etal-constraint-small-clades.phylip<br /> 3. Alignment partition file: Nakov-etal-tiger-partitions-rax<br /> 4. Character data for 540 diatoms and 2 Bolidomonas: Nakov-etal-542-taxon-discrete-characters.csv<br /> 5. The best tree from 420 RAxML optimizations: Nakov-etal-RAxML_bestTree.opt_89<br /> 6. 99 additional trees used in the analyses: Nakov-etal-99-randomly-sampled-unique-trees.newick<br /> 7. All 100 trees converted into chronograms: Nakov-etal-100-chronograms-smooth-1000.newick<br /> 8. Script with random seeds for RAxML optimizations: Nakov-etal-RAxML-calls-for-420-optimizations<br /> 9. R scripts with random seeds: Nakov-etal-R-scripts.zip (three scripts: equal-rates, independent, and coordinated + paint regimes models)<br /> 10. TreePL control file: Nakov-etal-TreePL-control-file.txt</p>