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If a new sequence is involved in the node and the sequence is not yet aligned in the previous steps, alignment calculation is performed.
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Reads were aligned using a multiple step alignment process.
Raw reads from all whole transcriptome RNA-seq libraries were aligned using a two-step alignment approach.
Except step alignment no reconstruction of the copper surface is observed.
Another method which does not require time alignment as a pre-processing stage is the iterative combination of a nearest neighbour search step and a conversion step alignment method (INCA) [12].
I do not find it logical that a two-step alignment has higher accuracy than a single step alignment, against what the authors claim.
Finally, we tested the full two-step alignment procedure using virtual trajectories.
Combined (Tophat + bowtie2) sequence alignment generated by the two-step alignment approach served as input file for HTSeq.
DACTAL's modular approach also allows us to replace each step (alignment, tree estimation, supertree estimation and even the dataset decomposition) with new approaches.
After the scan region step (alignment parameters at the default settings), reported references were sorted by the sum of mixed-ranking scores of all 13 genome regions.
In a next step alignments of the core genes are generated using MUSCLE, non-matching parts of the alignment are masked by GBLOCKS and subsequently removed.
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