“…For comparison, the same sequences were obtained for 9 isolates of which the genomes have been sequenced and are available in Genbank. The isolates CRT35 (NCBI reference sequence JFBI01000001; Massung et al, 2007;Al-Khedery et al, 2012) and CRT38 (NCBI reference sequence NZ_APHI00000000) were isolated from I. scapularis ticks, the isolate Dog2 was isolated from a dog (NCBI reference sequence CP006618; Al-Khedery et al, 2012), the isolate JM was obtained from a rodent (NCBI reference sequence CP006617; Al-Khedery et al, 2012), the MRK isolate was obtained from a horse (NCBI reference sequence JFBH00000000; Al-Khedery et al, 2012), the (Katoh and Standley, 2013). After alignment, regions with gaps were removed and 2354 gap-free sites were used in maximum likelihood (ML) phylogenetic analysis as implemented in PhyML (v3.0 aLRT) (Anisimova and Gascuel, 2006;Guindon and Gascuel, 2003).…”