Sentence examples for phylogenetic alignment from inspiring English sources
Nucleotide sequences were analysed and interpreted using Sequencher (Version 5.1, Gene Codes Corporation) and aligned relative to the rCRS [5] following phylogenetic alignment rules defined in [6].
In cases where only one species per family or order was present in the plot, the trnH-psbA sequence of that species was not included in the phylogenetic alignment.
The profiles of the EMPOP database are stored in position-based format relative to the rCRS following the rules proposed in [6] for phylogenetic alignment.
Phylogenetic alignment of the query string is derived from the alignment of the base profile of the EMPOP database and the transcript (Table 2).
The sequences of the TR were different and unique for each of the 30 genes identified (see the phylogenetic alignment of the tandem repeats in Additional file 2).
In the following sections we first describe the main concepts of our new method for phylogenetic alignment and placement of sequences using partial-order graphs.
Phylogenetic alignments and tree files are available from the Dryad Digital repository http://doi.org/10.5061/dryad.org/10.5061/dryad
The best fitting nucleotide substitution model for the phylogenetic alignments was inferred to be the Hasegawa Kishino Yano model with discrete gamma and invariant among-site rate variation.
We compared these 12 metrics with traditional diversity indices and compared among values from phylogenetic alignments varying from few to many plastid genes generated with high-throughput sequencing.
To distinguish whether positive selection acted directionally on the branch leading to the one or the other species for the genes identified by MKT, a likelihood approach depending on phylogenetic alignments was used.
It is absolutely true that in certain cases gene trees do not reflect gene evolution (i.e. due to recombination, domains fusions, unequal evolutionary rates affecting homology detection and excluding fast evolving sequences from phylogenetic alignments).
