Sentence examples for used for tree building from inspiring English sources
When using amino acid sequences, various methods used for tree building (including distance-based neighbor joining and maximum parsimony reconstructions) provided a similar topology, with VN strains appearing ancestral, separate clusters including VD and IN sequences and finally a large group of ID sequence that seemed to have emerged more recently from a common ancestor (see figure 10A).
These models were used for tree building, substitution mapping and parametric bootstrap simulations.
RAxML [ 65] was used for tree building with the evolutionary model parameter JTT+F+I+G and a bootstrap of 1000.
We have shown that the algorithm used for tree building is very robust when adding more sequences, with over 85% of the trees being completely unchanged and only 2% with major changes [ 10].
After manual inspection, alignments were used for tree building using MrBayes 3.2.2 [ 70] implemented in Geneious R6, using default parameter settings, with the exception of the rate matrix, for which wag was used.
It would be worth adding references and discussing some of the issues that arise when metatranscriptome and metaproteome data are used for tree-building purposes.
The longest dinoflagellate-derived Tic110 homolog, as identified by FastTree analysis, was used for final tree building as described above.
These were aligned using CLUSTALX [ 34] and edited so that only conserved blocks of residues were used for evolutionary tree building.
From the deduced amino acid sequences identified, phylogenies have been computed using the Phylogeny.fr platform [ 63], which uses MUSCLE for multiple alignment with Gblocks for alignment curation and the maximum likelihood PhyML method for tree building using the MEGA software 4.0 [ 64].
But MDL was used only to identify breakpoints, not for tree building.
The phylogenetic tree was produced using MUSCLE for multiple alignment, Gblocks for automatic alignment curation, PhyML for tree building and TreeDyn for tree drawing using the tree-generation pipeline at Phylogeny.fr website [ 54].
