Computational protocol: Torque Teno Sus Virus (TTSuV) in Cell Cultures and Trypsin

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Protocol publication

[…] The obtained sequences were aligned with two sequences proposed as TTSuV1 prototypes (accession no. AY823990 and AB076001) and one sequence proposed as TTSuV2 prototype (accession no. AY823991) available at GenBank , . A human TTV sequence was included in the alignment as outgroup (accession no. AB041007). Sequences were aligned using the ClustalW program within the MEGA 4 package. The construction of phylogenetic tree was carried out using the neighbor-joining (NJ) method in the MEGA 4 software package, based on Kimura two-parameter distance estimation method. Bootstrap resampling was performed for each analysis (1000 replications). […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Sus scrofa, Torque teno sus virus 1a, Torque teno sus virus 1b, Bos taurus