Web23 Dec 2016 · The parSNP tree is based on SNPs identified in the 1.2%–1.4% of the individual genomes present in all 346 genomes, representing ∼20 kb of the 1.6 Mb H. pylori genome, and was not further used. Pan-genome analysis of Helicobacter pylori. The 346 genomes were annotated using Prokka ... WebAntimicrobial resistance genes, plasmid replicons and pathogenicity islands were identified. A phylogenetic tree was constructed using Parsnp and was edited with FigTree. Results: The genome size of strain EC20120916 is 4 699 318 bp with a GC content of 55.2% and 4471 protein-coding genes. The aac(6')-laa gene, encoding resistance to ...
Parsnp :: Anaconda.org
Webthe topology of the resulting phylogenetic trees was very similar (Fig. 1). Although the order of specific serovars did differ, the 200 Salmonella genomes clustered into 10 different major groups matching the respective serovars in both parSNP and FFPry trees. The differences in order of the clusters between the FFPry and parSNP WebHowever, the EDGAR and Parsnp trees did not agree in their placement of genotype 2 subtypes. All four genotype 2 subtypes clustered separately from each other in the tree generated by EDGAR, with ... creating an anonymous form microsoft forms
Harvest — harvest 1.0 documentation
WebThe phylogenetic tree was created by comparison of core single-nucleotide polymorphisms identified using the ParSNP program [63]. Treegraph v2 [64], MEGA7 [59] and Figtree were used to annotate ... Webparsnp_tree - guide tree produced by Parsnp; max_merge_size - maximal merge size for guide tree compression; ... Note: The guide tree generated by progressiveMauve needs the addition file listing all genomes, because the guide tree does not contain the respective file names. The ordering of the genomes has to match the input ordering of ... Web2 Dec 2015 · The parsnp.tree file is the raw output generated by FastTree2, whereas the one you view within Gingr is after the Harvest import, where the adjustment occurs. This … creating an annotated bibliography