evogytis/ebolaGuinea2014

Phylogenetic analysis of 2014 Ebolavirus outbreak in Guinea. ##Phylogenetic analysis of 2014 Ebolavirus outbreak in Guinea. This repository contains three alignments (nexus format) and three trees (FigTree format) that were used by @rambaut and I in the PLOS Currents Outbreaks paper: - `ebolavirus_cds.nex` - contains 7 concatenated protein coding sequences from 49 ebolavirus genomes. This alignment was analyzed using MrBayes. The resulting tree `ebolavirus_cds.nex.con.tre` was used to make Figures 2 and 3. - `ebolavirus_intergenic.nex` - contains concatenated non-coding sequences from 49 ebolavirus genomes. This alignment was also analyzed in MrBayes. The resulting tree `ebolavirus_intergenic.nex.con.tre` was used to make Figure 4. - `ebolavirus_raw.nex` - contains 49 aligned complete ebolavirus genomes. This alignment was analyzed in PhyML and the resulting tree, `ebolavirus_raw.phyml.tree` was used to make Figure 1. ============== ###Acknowledgments We would like to thank Stephan Günther at the Bernhard Nocht Institute for Tropical Medicine, Hamburg and his co-authors for sending the 2014 Guinea outbreak sequences ahead of their publication on Genbank.