| Autor: |
Nova, Meryl Vila, Kévin Durimel, Kévin La, Felten, Arnaud, Bessières, Philippe, Michel-Yves Mistou, Mariadassou, Mahendra, Radomski, Nicolas |
| Rok vydání: |
2019 |
| DOI: |
10.6084/m9.figshare.10263833.v1 |
| Popis: |
Additional file 5. Topology differences of phylogenomic trees of Salmonella enterica subsp. enterica serovars (n = 440). The phylogenomic trees were reconstructed by maximum likelihood selecting the most appropriated models of evolution and checking ultrafast bootstrap convergences (i.e. IQ-Tree). The compared approaches ‘variants’ and ‘genes’ correspond to phylogenomic reconstructions based on pseudogenomes from variant calling analysis (i.e. iVARCall2) including (A) or excluding (B) recombination events (i.e. ClonalFrameML), and concatenated orthologous genes (C) from pangenome analysis (i.e. Roary), respectively. These graphical representations were produced with the cophylo function of the ‘phytools’ R package. Most of the branches of the trees (i.e. 85, 55 and 77% for approaches A, B and C, respectively) are supported by bootstrap values higher than 90% and the corresponding newick files are accessible under request. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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