Clustal W

[…] were sequenced on an abi 3130 (life technologies, carlsbad, ca, usa) capillary sequencer following standard protocols. sequence chromatograms were assembled into contigs, edited, and aligned using clustalw in geneious 8.1.7 (biomatters inc., auckland, new zealand). gene alignments were exported as fasta files for subsequent analyses. sequences are deposited in genbank under accession numbers […]

[…] 1)., reference 16s rrna and protein sequences for phylogenetic inference were obtained from the ncbi database. multiple sequence alignments of these sequences were generated automatically using clustalw2 (larkin et al., 2007). phylogenetic trees based on 16s rrna gene sequences were constructed using mega 6 software with the maximum likelihood algorithm (tamura et al., 2013). also, […]

[…] or more bootstrap percentages., figure s3 | specificity-determining positions alignment for the cp amino acid sequences of the geminiviridae family. (top) cp multiple sequence alignment colored by clustalx code. the sequences were automatically divided into 9 groups by sci-phy and sdps calculated by the speer server. colored boxes on the left indicate the different genus of the geminiviridae […]

[…] the empty vector (pcf430 or pze21-mcs)., the geneious software (version 6.0.5) (kearse et al., 2012) was used for sequence comparisons and phylogenetic analyses. for sequence alignments, we used clustalw (thompson et al., 2002), and the phylogenetic trees were inferred using maximum likelihood (jones et al., 1992). bootstrap values were calculated based on 100 replications. trees […]

[…] method31., amplification of the its region (its1-5.8s-its2) from the genomic dna of the species under study was conducted via pcr using its-1 and its-4 primers. the sequences were aligned using clustalw32 implemented in the mega7 program33. the phylogenetic analyses were performed in mega7 using the neighbour-joining method34 with 1000 bootstrap replicates35 for each analysis. pairwise […]