Analysis of the phylogeny of M. tuberculosis strains collected as part of a prospective observational Exit_Rif study

EvolView (http://www.evolgenius.info/evolview) and iTOL (http://itol.embl.de) are online tools for displaying, managing and customizing phylogenetic trees. With tese tools, you can: visualize phylogenetic trees of various formats, add datasets and do customizations to phylogenetic trees, export trees to various text (newick, nhx, phyloXML, etc) and graphic formats, and organize trees, projects and datasets in an intuitive and efficient way.

EVolview_script.py: generate evolview scripts to plot parameters from VCF file and metadata on the tree

add_lineage_to_Id.py: add lineage to sample-id in a tre or fasta file

raxml.py: create an alignment file from all the fastas and run raxml

iTOL_script.py: generate iTOL scripts to plot parameters from VCF file and metadata on the tree

Please cite these scripts as follows: S. Kalboussi & T.H. Heupink,Phylogeny,(2017), https://github.com/sondekalboussi/CWGSMTB