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Fig. 5 | BMC Genomics

Fig. 5

From: Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens)

Fig. 5

Phylogenetic tree based on SNPs (single nucleotide polymorphisms) of Mycobacterium tuberculosis Complex (MTBC) using Maximum Likelihood (ML) model. Green box: modern cluster 1; orange box: modern cluster 2; pink box: ancient cluster; black circle: deletions MiD3 and MiD4; red triangle: deletion RD2seal. Mycobacterium tuberculosis H37Rv was used as outgroup. A customized script in Python version 3.6.3 was used to build a matrix of SNPs, which was used to infer a ML tree using RAxML with GTRCAT model and autoMRE for best-scoring ML tree and a maximum of 1000 bootstrap inferences using RaxML software version 7.3

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BMC Genomics

ISSN: 1471-2164

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