Thus, it is inaccurate to assess NetDis, an alignment-free approach, in comparison to an alignment-based approach, due to the difference in the goals of the two approach categories.
Introns were identified by comparison to gene alignments of other algae and representative bryophytes.
Thus, here we systematically and fairly evaluate the performance of NetDis in comparison to other alignment-free network comparison methods, and address all issues present in the paper by Ali et al.
In comparison to the TS3.4 alignments, TS2.0/2.2 alignments contain more mismatches, exhibit higher variation in size and have more erroneous gaps proximal to the indel position (Additional file 1: Figure S1).
Inspection of the alignment and comparisons to similar alignments produced using CLUSTALW [ 16] showed that the MUSCLE alignment was better at correctly aligning the zinc coordinating amino acids and fewer manual adjustments were required than with CLUSTALW results (data not shown).
These subgroups first were aligned in CLUSTAL X [ 56], and the resulting sub-alignments then were aligned with each other and adjusted through visual inspection and comparison to the kinase alignment of Liu and Kipreos (2000) [ 32].
Output of the -S -n 1 -T options contains alignments truncated to the largest open reading frame and, by comparison to the full alignment output (-S -n 1 options), allows the calculation of the untranslated regions (UTRs).
In comparison to the traditional alignment concept, which defines pairwise mappings between the coordinates of the involved sequences, the SuperGenome has the advantage that independent alignment blocks are combined into a global coordinate system.
Prank-codon has performed best in comparison to other multiple alignment tools (Fletcher and Yang 2010), such as Mafft (Katoh et al. 2002), Muscle (Edgar 2004) and ClustalW (Thompson et al. 2002), and prank-aminoacid was used for obtaining input files for downstream positive selection studies.
This approach drastically reduces the number of alignments computed in comparison to more general, global alignment searches [ 10], as will be shown later in the " Results and discussion" section.
