Xanthomonas citri - 36 strain concatenated genome alignment (gaps +/- 20nt removed) FASTA format, Contains recombination

A FASTA format multiple sequence alignment used for phylogenetic reconstruction. The alignment was constructed by concatenating blocks from a whole genome multiple alignment using the IAPAR 306 strain to order blocks. Gap-containing columns and 20 nt surrounding gap-containing columns were removed. The alignment contains regions of recombination and the distibution of A pathotype strains is reduced to only those containing recombination event 16

Xanthomonas citri - 36 strain PhyML phylogeny GTR model, Reduced A-strain distribution, Contains recombination

A maximum likelihood phylogenetic tree constructed with PhyML from the genome alignment of 36 strains of Xanthomonas citri. The alignment contains regions of recombination and the distibution of A pathotype strains is reduced to only those containing recombination Event 16. The evolutionary model used was GTR

Xanthomonas citri - 44 strain PhyML phylogeny SYM model

A maximum likelihood phylogenetic tree constructed with PhyML from the genome alignment of 44 strains of Xanthomonas citri. Regions of recombination were removed from the alignment as well as gap-containing columns and +/- 20bp from a gap-containing column. The evolutionary model used was SYM, as chosen with jModeltest 2.1.7

Additional file 6: of Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges

Pathotype-specific significantly enriched or depleted ( P <0.05) COG categories for missing genes, SNP-containing genes or genes within zones of recombination. (XLSX 12 kb

Xanthomonas citri - 44 strain concatenated genome alignment (recombination, gaps +/- 20nt removed) FASTA format

A FASTA format multiple sequence alignment used for phylogenetic reconstruction. The alignment was constructed by concatenating blocks from a whole genome multiple alignment using the IAPAR 306 strain to order blocks. Regions of recombination detected using RDP were removed, as were gap-containing columns and 20 nt surrounding gap-containing columns

Xanthomonas citri - 44 strain Mugsy genome alignment

A multiple genome alignment of 44 strains of Xanthomonas citri output from the Mugsy genome alignment softwar