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Fig. 2 | Standards in Genomic Sciences

Fig. 2

From: Draft genomes of “Pectobacterium peruviense” strains isolated from fresh water in France

Fig. 2

Phylogenetic trees of “P. peruviense” strains and strains of other Pectobacterium species and subspecies. a Phylogenetic tree constructed from the gapA nucleotide sequences. Sequences were aligned using the MUSCLE software [24] and the alignments were filtered by using the program GBLOCKS [25].Tree was computed using PHYML [26]. One hundred bootstrap replicates were performed to assess the statistical support of each node. Bootstrap support values (percentages) are indicated if superior to 95%. gapA sequences were retrieved from full genome of type strains (accession numbers are indicated in Fig. 1b) or obtained from the sequenced gapA amplicon for strains A97-S13-F16 and A350-S18-N16. b Phylogenetic tree constructed from concatenated sequences of 1266 homologous amino acid sequences. Before concatenation, the homologous sequences of each gene were aligned using the MUSCLE software [24] and the alignments were filtered by using the program GBLOCKS [25]. Tree was computed using PHYML [26]. One hundred bootstrap replicates were performed to assess the statistical support of each node. Bootstrap support values (percentages) are shown if less than 100%. The accession number for each genome is indicated inside brackets after the strain name. Dickeya solani RNS08.23.3.1.A was used as outgroup. Type strains are marked with T after the strain name

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