For each of these multiple alignments, trees were also generated, as described above.
Clearly, the visualized network gives more information about how these sequences fit into the larger context of the superfamily than can be conveyed by a listing of scores or even a multiple alignment or tree.
By sequence similarity, multiple alignment, and tree-reconstruction approaches, we investigate the phylogenetic relationships among the PWWP domains of proteins from the genomes of species with established evolutionary relationship within the plant and metazoan lineages (see Additional file 1 and Additional file 2) [ 29, 30].
SB performed all of the multiple alignments and tree constructions.
Yet, multiple alignments and tree reconstructions with hundreds of thousands to millions of environmental sequences from HTS are either slow (when accurate) or inaccurate (when fast) [ 44].
Multiple alignments, phylogenetic tree constructions and laterally transferred gene mining were carried out using a gene mining pipeline that we developed in a previous study [ 28].
This evidently shows that the classical approach of multiple alignment followed by tree reconstruction is superior only if the alignment is correct.
The produced multiple alignment and phylogenetic tree can be easily displayed online or downloaded for further offline analyses.
We also run Motiph as a simple PWM scanner to scan just the S.cerevisiae intergenic regions, ignoring the multiple alignment and evolutionary tree.
Included in the multiple alignment and phylogenetic tree is a group of seven strains widely used in the laboratory (S288c, W303, RM11-1a, FL100, Sigma 1278b, SK1, Y55), several of which are known to be closely related (Winzeler et al. 2003).
