T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.
This can be explained by the quadratic time complexity of the DP-based alignment computation and the increasing number of seeds for longer reads.
We also present an efficient new segment-based alignment algorithm for time series called SCOW (shorting correlation-optimized warping).
Then this protein based alignment was converted to the codon-based alignment with PAL2NAL [ 45].
On cross-validation, the extent of cortex that shows correlated time courses of neural activity while watching a movie increased by 26% after function-based alignment.
To develop a real-time alignment monitoring system (RAMS) to compensate for the limitations of the conventional room-laser-based alignment system.
Whereas the anatomy-based alignment maximizes correspondence of indices of cortical curvature, our method maximizes correspondence of functional time-series for each cortical node.
Fiala, J. C. & Harris, K. M. Computer-Based Alignment and Reconstruction of Serial Sections.
Papadopoulos, J.S. & Agarwala, R. COBALT: constraint-based alignment tool for multiple protein sequences.
