Computational protocol: The first isolate of Candida auris in China: clinical and biological aspects

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Protocol publication

[…] The internal transcribed sequences (ITS) of C. auris BJCA001 and previously reported isolates were aligned using mafft v7.015b. The Maximum- Likelihood phylogenetic tree was generated using RAxML v7.3.2. The General Time Reversible (GTR) model and Gamma distribution with Invariant sites (Gā€‰+ā€‰I) were adopted. Schizosaccharomyces pombe strain ATCC 38366 was used as an outgroup, whereas Candida pseudohaemulonii_CBS10099T, Candida duobushaemulonii_CBS7798T, and C. haemulonis_CBS5149T served as comparators. To better illustrate the phylogenetic position of C. auris, several other Candida species were also included. The ITS sequences of the reported strains were acquired from the GenBank ( or CGD ( databases directly or extracted from the genome sequences. […]

Pipeline specifications

Software tools MAFFT, RAxML
Application Phylogenetics
Organisms Homo sapiens, Fungi, [Candida] auris, Candida albicans, Mus musculus, Galleria mellonella
Chemicals Amphotericin B, Sodium Chloride, Fluconazole, Copper Sulfate