This archive includes data and result files relating to: Grimm GW, Morrison D Trees and viruses: the SARS group Genealogical World of Phylogenetic Networks. Posted 30/3/2020 http://phylonetworks.blogspot.com/2020/03/trees-and-viruses-sars-group.html and follow-up posts Topfolder -- XLSX-formatted tabulation of harvested data including a heat-map based on uncorrected distances. Folder Harvest -- FASTA-formatted mafft (Katoh & Stanley 2013)-aligned data (uncurated) harvested from gene banks per 13/3/2020 Folder Mats Matrices used for analysis Corona.mafft.nex -- NEXUS-formatted full alignment, pre-aligned with mafft and manually adjusted, not used (unalignable or poorly aligned for some groups) gene regions annotated. To view annotation, open the file with Mesquite. Corona.simple.nex -- Simple (old) NEXUS-formatted full alignment, with PAUP* definition lines and code blocks. CoronaNoDupl.* -- Literal duplicates and not globally aligned regions eliminated. Matrices used for analyses. CoronaNoDuplFull.* -- Literal duplicates eliminated, but including non-aligned bits. Only to be used for visual inspection only. Corona.CoV2only.* -- CoV-2 subset. *.nex -- Mesquite-version; empty columns removed, alignment numbers are same as those reported in the CoV-2 genotyping spread-sheet. *.simple.nex -- Version including PAUP* definition lines to exclude positions irrelevant for inferring Median networks. *.PIP.epf -- (extended) PHYLIP-formatted export including only parsimony-informative patterns *.VP.epf -- (extended) PHYLIP-formatted export including all variable sequence patterns within the CoV-2 subset (indels represented by single site) *.c.* -- strict consensus sequences computed with g2cef (Göker & Grimm 2008) *.v.* -- modal consensus sequences computed with g2cef *unc.dist -- Splits-NEXUS-formatted uncorrected pairwise-distance matrix and neighbour-net splits graph Folder ML RAxML analysis files (see manual for file naming conventions) *group.c -- using strict group consensus sequences *group.v -- using modal group consensus sequences *guide -- guide tree analysis using non-consensed data (literal duplicates eliminated) *_check.xx -- List of literal duplicates eliminated by RAxML during pre-analysis check-up *25plus.nxs -- Splits-NEXUS-formatted bootstrap consensus networks using a split frequency cut-off of 25 (Holland & Moulton 2003, Schliep et al. 2017) Cited literature Göker M, Grimm GW. 2008. BMC Evol. Biol. 8:86. http://www.biomedcentral.com/1471-2148/8/86 Holland B, Moulton V. 2003. In: Benson G, and Page R, eds. Algorithms in Bioinformatics: Third International Workshop, WABI, Budapest, Hungary Proceedings. Berlin, Heidelberg, Stuttgart: Springer Verlag, p. 165–176. Katoh K, Standley DM. 2013. Mol. Biol. Evol. 30:772–780. Schliep K, Potts AJ, Morrison DA, Grimm GW. 2017. Methods Ecol. Evol. 8:1212–1220. http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12760/full