Pyrotools

[…] ). the sequences were used as queries to search ncbi and phytozome () databases for sofl homologs using blastp option using a < 1 x 10-2 cut-off value. the amino acid sequences were aligned using probalign v1.3 () on cipres science gateway server (). bayesian inference analysis was performed with the mr. bayes 3.2.1 on xsede tool on cipres science gateway for 30 million generations with 8 […]

[…] for testing positive selection. a further 400 mcl clusters were unable to produce alignments that contained continuous sequence for all eight species, leaving 932 genes that were used as input for probalign to build consensus quality alignments. probalign does an additional filtering by removing poor quality alignments, and we further required all alignments to cover > 50% of the sites […]

[…] nonetheless, the resolution was slightly improved and the positions of most genes were better congruent with angiosperm phylogeny. in contrast, the dataset created based on an alignment produced by probalign only included 696 sites, among which 591 were informative (dataset ). moreover, in the resulting phylogenetic tree, the positions of some major plant groups were discordant with angiosperm […]

[…] parameter of 1.8. simulations have shown this value to be generally robust to false positives and negatives (). nucleotide sequences corresponding to each mcl gene cluster were aligned using probalign v1.1 ()., for the phylogenetic analysis, we selected those mcl gene clusters that were shared among all taxa and contained only single gene copies for each taxon (the core set) (n = 159) […]

[…] rrna gene fragments from b. bovis (eu075182) and t. parva (z23263) were used as a query under suggested algorithm parameters [] in ncbi blast 2.2 []. in silico analysis was also performed with probalign beta version 1.2 [] and ssearch 3.5 [] using known rrna gene fragments and suggested advanced search options [,]. newly identified candidate rrna genes were, likewise, used as input […]