Computational protocol: Ecological scenario and Trypanosoma cruzi DTU characterization of a fatal acute Chagas disease case transmitted orally (Espírito Santo state, Brazil)

Similar protocols

Protocol publication

[…] The sequences were edited, aligned and corrected using the BioEdit software. The sequences were compared with nucleotide sequences deposited in GenBank using the BLAST (Basic Local Alignment Search Tool) algorithm. Phylogenetic tree construction was performed using Mega 5 software []. We used the maximum likelihood (ML) method, employing the best DNA model. The best substitution model was identified as having the lowest Bayesian Information Criterion  score (BIC): Hasegawa-Kishino-Yano for the 1f8 gene, Tamura 3+ G (a gamma-distributed rate of variation among sites) parameter for the GPI gene, Kimura 2-parameter for the 18S rRNA gene, and the Kimura 2 + G parameter for V7V8 SSU rRNA, with bootstrapping at 1000 replicates. We used T. cruzi (TcI to TcVI), T. c. marinkellei, T. rangeli and T. dionisii sequences from GenBank as references. All sequences analyzed were deposited in the GenBank database under the accession numbers KR905432–KR905446 for the 18S rRNA marker, KT737478 for GPI and KT983981 for 1f8. The GenBank accession numbers can be viewed in Additional file .Fig. 2 […]

Pipeline specifications

Software tools BioEdit, BLASTN, MEGA
Application Phylogenetics
Diseases HIV Seropositivity, Infection, Coinfection
Chemicals Chloroform, Xylenes, Phenol