The new transition kernel uses the SPR operator to propose new trees, but is extended to be alignment-aware.
Overall Splign appears to be a robust program with excellent accuracy, and a very useful "splice site aware" alignment algorithm.
There are ways to align bisulfite colorspace sequences with methylation-aware alignment approaches, which convert bisulfite colorspace sequences to basespace and index all theoretically possible alignments by creating a hash table.
Rip sequences were aligned using the ProGraphMSA program, which implements the evolution-aware alignment [ 65, 66].
After demultiplexing, 36 bp RNA-Seq reads were trimmed from barcodes (4 nt) and mapped to the TAIR10 reference genome including known variation with the PALMapper aligner (Jean et al., 2010) using a variant-aware alignment strategy.
In fact, these data could be used to create structurally aware alignments of the sequences, using structural information for only one or a few members of the protein family (see Figure S2).
Data is not presented on the myosin alignment for tree-aware methods which proved too computationally intensive to be practical.
While a second, allele-aware alignment increases accuracy at predicted heterozygous sites, these modest gains, still accompanied by a high rate of false discovery, require an additional alignment.
Results: We have developed a method for phylogeny-aware alignment of partial-order sequence graphs and apply it here to the extension of alignments with new data.
Here, we outline a new general-purpose method for phylogeny-aware alignment of sequence graphs and apply it to phylogenetic extension of existing alignments.
We have generalized the concepts of our phylogeny-aware alignment algorithm and developed a method for phylogenetic alignment of partial-order sequence graphs.
