SeaView

[…] 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 [13–15]. 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 program55, 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 […]

[…] errors due to nucleotide misincorporation and/or recombination., all sequences generated in the present study have been registered in genbank (kp747713–kp748171)., dna sequences were assembled with seaview (gouy, guindon, & gascuel, 2010), aligned with mafft v.7 (katoh & standley, 2013) and manually checked and cleaned using gblocks (castresana, 2000) when necessary (cab11). the cpdna […]

[…] low-confidence regions were removed with gblocks (v.0.91b) (56) to produce a sequence matrix of 138,476 amino acid sites. both phylogenetic trees (fig. 1b and c) were made from this alignment with seaview (v.4.6.1) (57). the distance tree was generated by neighbor joining with bionj (58) and the kimura distance model (38). the maximum-likelihood tree was generated with phyml (v3.0) (39) […]

[…] phylogeny with the maximum likelihood algorithm (ml) in the mpi-parallelized version of raxml version 7.3.0 (stamatakis, 2006). ambiguous alignments were removed using the gblocks method in seaview (gouy et al., 2010) with options for a less stringent selection. the lg model (le and gascuel, 2008) with a proportion of invariable sites (+i), a gamma-shaped distribution of rates across […]