Sentence examples for matrices and tree from inspiring English sources

The nucleic acid matrices and tree for phylogenetic analysis can be found in TreeBASE website at this link http://purl.org/phylo/treebase/phylows/study/TB2 S18029?x-accesscode=2a8e85af14b2eb2378b3d6c838f1fa90&format=html.

We performed a concatenated analysis of the 277 low-copy nuclear loci in RAxML 8.1.3 (Stamatakis, 2006), using an unpartitioned GTR-GAMMA model and with support quantified by 5000 bootstrap replicates (matrices and tree files for the analyses of this paper available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.4cn66 [ Folk et al., 2015]).

All matrices and trees are available from TreeBASE (http://purl.org/phylo/treebase/phylows/study/TB2 S11444).

Targeted nuclear exon sequences, data matrices, and trees were submitted to Figshare (http://dx.doi.org/10.6084/m9.figshare.org/10.6084/m9.figshare

All taxa information, matrices and trees have been made available through TreeBASE at the following URL: http://purl.org/phylo/treebase/phylows/study/TB2 S15946.

The aligned sequences were exported for phylogenetic analyses as separate data matrices of nucleotide sequences and amino acid sequences, and all data matrices and trees were deposited in TreeBASE (Study accession S1459, matrix accessions M2623-M2624) [ 45].

The aligned matrices and trees of the Galerucella analyses (nuclear dataset and COI + nuclear dataset) and the Asecodes analysis (COI + nuclear dataset) are available at TREEBASE under URL http://purl.org/phylo/treebase/phylows/study/TB2 S14144.

After the maximum tree value had been obtained, the pruning process began in order to obtain optimum tree set, using the cost-complexity setting method, providing the balance between probability of misclassification calculation from risk matrix and tree complexity.

The results were plotted as a similarity matrix and tree showing the phylogenetic distances and relationships between the analysed strains.

Phylogenetic analyses were performed using Cas9/Csn1 sequences aligned with ClustalX2 (Larkin et al. 2007), and distance matrix and tree construction using Phylip 3.69 and MEGA 5.2.1 (Felsenstein 1989; Tamura et al. 2011).

In all MP analyses, multistate characters were treated as polymorphic, indel characters embedded in the sequence data matrix were treated as missing data (but were represented in an additional character matrix), and tree searches using PAUP [ 23] were heuristic using at least 200 random addition replicates and TBR branch-swapping.