SeaView

[…] d OBPs and CSPs from T. elegans and other Hemipteran species were performed using MAFFT (http://mafft.cbrc.jp/alignment/server/clustering.html), and phylogenetic trees were constructed using PhyML in Seaview v.4 using the Jones-Taylor-Thomton (JTT) model with 1000-fold bootstrap replication in neighbor-joining method (NJ). […]

[…] up to a 96% identity were downloaded and included in the phylogenetic analyses. For comparative purposes all the sequences used in the Amills et al. [] study were included. Sequences were aligned in Seaview v.4.2.11 [] with ClustalW2 [] default settings. The best substitution model for the Bayesian inference (BI) analysis was identified using the Bayesian information criterion (BIC) in jModeltest […]

[…] The methodological approach of was followed in order to estimate individual gene trees and a supertree. We have used MAFFT 7 () to individually align the molecular markers and SeaView 4 () to manually adjust them. Bayesian analysis was conducted in MrBayes 3.2.2 (, ) for individual gene trees (Fig. , Suppl. material ) using the GTR + G substitution model. The Markov chain M […]

[…] nomes was build using the Phylogenetic Tree service included in the PATRIC genomic platform (). Phylogenetic trees for the selected protein families were constructed via the PhyML algorithm () in the Seaview software (), using the default parameters and bootstrap values computed with 100 replicates.The comparative genome analysis and reconstruction of arabinose and AOS utilization pathways were pe […]

[…] the Los Alamos National Laboratory (LANL) website (http://www.hiv.lanl.gov/content/sequence/GENE_CUTTER/cutter.html) and then refined manually. Full-length envelope sequences were manually edited in Seaview []. The infant T/F env virus sequences were identified by analysing phylogenetic trees and highlighter plots, and infant consensus sequences of the major T/F lineage were generated using the L […]

[…] ned with MAFFT v.7.299b [] and the fast and progressive method FFT-NS-2, suitable for large alignments. One inverted repeat region (IRa) was excluded from the alignment. The alignment was viewed with SeaView v.4.6 [] or Mesquite v.3.10 [] and subsequently processed with GBLOCKS v.0.91b [] using default parameters, which stringently trims alignments allowing no gaps. Hence, the final dataset only i […]