Harvest and phylogenetic network analysis of SARS virus genomes (CoV-1 and CoV-2)

Data and analyses relating to:<br>Grimm GW, Morrion D (2020). Trees and viruses: the SARS group. <i>Genealogical World of Phylogenetic Networks, </i>posted 30/3/2020<i>.</i>http://phylonetworks.blogspot.com/2020/03/trees-and-viruses-sars-group.html<i><br></i><i><br></i>Grimm GW (2020a). Using Median Networks to study SARS-CoV-2. <i>Genealogical World of Phylogenetic Networks, </i>posted 20/4/2020.https://phylonetworks.blogspot.com/2020/04/using-median-networks-to-study-sars-cov.html<br><i></i>Comment to Forster et al. (2020), <i>PNAS</i>, doi: 10.1073/pnas.2004999117 <br><i></i>The main 7z-archive [7z.org/Wikipedia] includes all used data (non-curated gene bank harvest, curated alignment) and analysis files in standard phylogenetic data formats (FASTA, NEXUS, NEWICK, Splits-NEXUS). For labelling conventions and archive content see ReadMe.txt.<br>New in Version 2: Fully annotated genotype spread sheet, <i>CoV2Genotyping</i> (XLSX) of the CoV-2 subsample included in our original harvest tabulating particular and general mutations patterns. The main archive has been updated.<br>New in Version 3: Archive <i>Hack-and-Fish.7z </i>including analysis files for the experiment described in this post:Grimm GW (2020b). Hack and fish ... for recombination in the SARS group. <i>Genealogical World of Phylogenetic Networks</i>, posted 8/6/2020. https://phylonetworks.blogspot.com/2020/06/hack-and-fish-for-recombination-in-sars.html <br><br><b>Figures</b><i>MLTreeStrictGrCons—</i>Maximum likelihood tree based on strict group consensus sequences and branch support established via non-parametric bootstrapping<i>NNetCPlusRecomb—</i>Uncorrected <i>p-</i>distance (Hamming) based planar phylogenetic network based on the (strict) group consensus<br>data. Coloured lines refer to shared sequence patterns as visible from the alignment (likely recombination events)<i>NNetPlusSupport—</i>Uncorrected <i>p</i>-distance (Hamming) based planar phylogenetic networks based on the non-consensed (original) data (in total, 291 near-complete virus genomes) used to define major groups for consensing approach. Bottom-right, bootstrap consensus network for the same data.<i>MutationPatterns1, ...2—</i>Visualisation of mutation patterns that are either the consequence of homoplasy, i.e. convergent mutation from C to U in independent CoV-2 sublineages, or recombination. See 2^nd post (Grimm, 2020a) for further details. <i>HnS.All.sumCNet, HnS.All.sumBSNet</i>—Consensus networks of nine bit-wise ML trees (...CNet, strict) and according, pooled ML bootstrap pseudoreplicate trees (...BSNet, only splits with a frequency ≥ 20%). See 5^th post (Grimm, 2020b) for explanations.<br><br>Referenced and further related posts are linked below. <br>Comments are welcomed; please use the comment option at our blog Genealogical World of Phylogenetic Networks.<br>