Computational protocol: Genetic diversity of STLV-2 and interspecies transmission of STLV-3 in wild-living bonobos

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Protocol publication

[…] Newly derived nucleotide sequences were compared with previously published PTLV reference sequences. Sequences were aligned using MEGA 4 (), and where necessary, minor manual adjustments were performed. Sites that could not be aligned unambiguously or that contained a gap in any sequence were excluded from the analyses. Maximum likelihood (ML) trees were constructed using PhyML (, with 100 bootstrap replicates ().The TrN93 models with a gamma distribution across sites was the most appropriate model according to TOPALI () and was used for ML analyses for STLV sequences. […]

Pipeline specifications

Software tools MEGA, PhyML, TOPALi
Databases ATGC
Application Phylogenetics