SeaView

[…] database (the sequences are available upon request). we also included four eiv h3n8 ns sequences that we sequenced for this study (accession numbers mf182460, mf182451, mf182443, and mf182459) (40). seaview version 4.6.1 (41) was used to align the ns1 coding regions, and the final alignment was edited manually. nep coding regions were removed from the alignment. we used beast version 1.8.4 (42) […]

[…] curated by the los alamos national laboratory hiv sequence database (http://www.hiv.lanl.gov) was generated using muscle [49, 50]. neighbor joining and maximum likelihood trees were constructed with seaview 4 [51] and visualized with figtree 1.4.2. genetic distance analysis within each sample were conducted using mega 6 [52] and is expressed as substitutions per nucleotide (s/nt). the number […]

[…] were obtained from the genbank database. the sequences were aligned using clustalw, and a phylogenetic tree was constructed by using the phyml method in seaview 4 (http://pbil.univ-lyon1.fr/software/seaview) with the approximate likelihood ratio test based on a shimodaira-hasegawa-like procedure which used general time reversible as a substitution model. nearest-neighbor interchange, subtree […]

[…] -n automre, version 8.1.17). the amino acid substitution model lg [110] with empirical amino acid frequencies and 200 replicates for bootstrapping were assigned. the phylogenetic tree was drawn by seaview [111] (version 4.4.2)., low complexity regions of the d. coronatus proteins were masked by segmasker [112] (version blast 2.2.25). the d. coronatus proteins were searched for the c. elegans […]

[…] and (iv) cdna consensus sequences prepared from the mapped transcriptomic reads. clustalw alignment was implemented within the bioedit program [41]. a phylogeny nj tree was constructed using the seaview program [42]. all calculations were run at default conditions using the jukes-kantor model and 1000 replicates., phylogenetic nj trees were constructed from illumina reads using short 70 bp […]