Séance combines the alignment extension and phylogenetic placement capabilities of the Pagan multiple sequence alignment program with a suite of tools to preprocess, cluster and visualise datasets composed of many samples.
Because it is not feasible yet to index a large genome (more than 4 Gbp) by Subread, we had to split the wheat reference genome AABB into sub-genome A and sub-genome B, and then combine the alignment results using the following method.
Final computation of the likelihood score When all reads are properly aligned to the new version of the assembly, we can combine the alignments to the final score.
Finally, it combines the alignments from the original FastBLAST databases with the new alignments to produce a new FastBLAST database.
Here, we combined the alignment-based programs geneconv and PhiPack to detect genes affected by recombination between or within species.
The MULTIZ approach first runs all-against-all pairwise LASTZ alignments (default settings), followed by projections ensuring that the reference species is "single-coverage," with projection steps guided by the species dendrogram to progressively combine the alignments.
Because CSSS and PhymmBL are both hybrid models that combine the alignment-based and the alignment-free/composition-based approaches, in Supplementary Table S4 in Supplementary Data we compare the performance of the CSSS model to that of PhymmBL when BLAST scores are used for classification alone.
T-Coffee calculates pairwise alignments by combining the direct alignment of the pair with indirect alignments that aligns each sequence of the pair to a third sequence.
Therefore, the optimal performance of AMPs predictor can be obtained by combining the sequence alignment and SVM-LZ complexity pairwise algorithm.
Thus, in this study, a new algorithm for AMPs prediction is proposed by combining the sequence alignment method, Lempel-Ziv (LZ) complexity [ 17], and support vector machines- (SVMs-) pairwise algorithm [ 18, 19].
