SeaView

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

[…] to amplity pepper cryptic virus 2 (pcv-2) rna 1, dprimers to amplify pepper cryptic virus 2 (pcv-2) rna 2, for phylogenetic analysis, multiple alignments were performed by muscle implemented in seaview v.4.5.4 and the phylogenetic trees were built by phyml software [–]. maximum likelihood was used as the criterion to infer phylogenetic relationships between the isolates. the appropriate […]

[…] by using the blastp algorithm. the mtcra2 lrr-rlk, previously functionally characterized in m. truncatula regarding symbiotic nodulation, was also included. to generate a similarity tree using the seaview version 4 program, complete amino acid sequences of mtsunn and mtnrlk1 as well as the a. thaliana and m. truncatula closest related sequences previously identified were used to generate […]

[…] comparison by log-expectation (muscle) program (v. 3.8.31) [] was used to produce a multiple sequence alignment for each set of proteins. alignments were then manually corrected and masked in seaview (v. 4.2.4) []. sequences that required a high level of site exclusion (due to the sequence not aligning or not masking well) or where they formed long branches in preliminary analysis […]

[…] were added to the sequences of abundant or ubiquitous phf otus. the v1–v3 regions of these sequences were aligned with mafft v7.123b () and a maximum likelihood tree was inferred using the software seaview () with 1000 bootstrapped trials., the correctly formatted amplicons and clone libraries of five serpentinizing ecosystems were downloaded from public databases (sra and genbank). these data […]

[…] 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) […]

[…] material : table 1., 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]