Act10 with one single residue exchange only (D2E) is more distant, which reflects the scores in the permutation matrix used by the alignment program.
First, the initial guide-tree produced by the alignment program is highly similar to the canonical tree (Supplementary Fig. S6), indicating that it carries a strong phylogenetic signal.
We presume that this is a consequence of the k-mer (k = 25) assembly process used by Trinity, perhaps creating isoform transcripts that are shorter than the long 454 reads from which they originally derive or possibly from read trimming by the alignment program.
Second, the guide-tree reconstructed by the alignment program is generally a better estimator of the true topology than the tree reconstructed from gap patterns (Supplementary Fig. S6), indicating that the use of gap parsimony recovers less phylogenetic information than that already contained in the guide-tree.
Importantly, data structures and formats for all services are standardized, so the same client can submit data to, and handle the results from any of the alignment programs provided by any JABAWS MSA server.
Multiple sequence alignments produced by the three alignment programs ClustalW (a), MAFFT (b), or T-Coffee (c) are shown for a region containing the A-tract and the Q-tract in the lamprey Emx sequences that are indicated with gray background.
The distance and contact restraints in the second-round TASSER are taken from the combination of the centroid structures and the PDB structures searched by the structure alignment program TM-align [ 40] based on the cluster centroids.
More pronounced topology-level improvements were achieved when new structural templates identified from the PDB were incorporated into the folding iterations; these templates were detected by the structure alignment program TM-align [ 6], which matches the TASSER models with each of the known proteins in the PDB to identify the templates that are structurally closest to the TASSER models.
Promoters of orthologous gene pairs were aligned by the local alignment program water from the EMBOSS package [ 33].
