Sentence examples for matrices and trees from inspiring English sources
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 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.
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].
This article is organized as follows: we provide preliminaries and formulate the problem; in sections 3 and 4, Matrices and trees, and Extended tree following Gusfield, 12 we construct a tree for every matrix and discuss its properties.
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]).
The data matrix and trees have been deposited in TreeBASE (http://www.treebase.org; study number 12339).
The phylogenetic matrix and trees are available from Treebase (http://purl.org/phylo/treebase/phylows/study/TB2 S17255).
The data matrix and trees have been deposited in TreeBase ([ 28]; http://purl.org/phylo/treebase/phylows/study/TB2 S12505).
