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MOESM3 of The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium

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posted on 18.10.2019, 09:26 by Hirokazu Yano, Haruo Suzuki, Fumito Maruyama, Tomotada Iwamoto
Additional file 3. Phylogenetic trees based on codon alignments of marker gene candidates and hsp65. (i) MAH_0788/MAV_0940 ortholog, (ii) MAH_0771/MAV_0930 ortholog, (iii) MAH_0766/MAV_0925 ortholog, (iv) MAA_0809/MAV_0960 ortholog, (v) MAH_2714/ MAV_2410 ortholog (inadequate marker gene), (vi) hsp65 ortholog, (vii) MAV_1375 ortholog, (viii) MAV_2820 ortholog Trees were constructed using the GTR + G model in PhylML with 100 times bootstrapping run. Values by the branch indicate the number of bootstrap supports. Allele of strain A5 was used as an out group for the analysis in panels i–vi. The out group was not used for tree construction in panels vii and viii. Alignment information is shown by the tree as follows: n.allele, number of alleles in the alignment (population); nuc.diversity, average pairwise nucleotide diversity (number of site differences) in the alignment; hap.diversity, probability of haplotype (allele) differences in the alignment; alignment length, length of alignment without gaps.


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