Evolutionary and epidemiological analysis of Roka HIV outbreak
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Maximum likelihood phylogenies for HCV

This directory contains files for inferring maximum likelihood phylogenies for HCV1b and HCV6e. Files with bootstrap are the highest likelihood trees from raxml with bootstrap support values for all nodes in the tree. Files with figtree_reroot are the same files but have been re-rooted with the best fitting root (as determined in path-o-gen). These are the input files used for the figure creation.

ML tree for HCV1b and HCV6e