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The authors stress that they used a very long alignment (21,313 bp), that inner nodes got high support values, and that support for a close relationship between myriapods and chelicerates is consistent.
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Considerable parts of the ITS were not identically aligned between these three approaches, including a very long alignment-ambiguous part of the ITS1 and two shorter alignment-ambiguous parts of the ITS2.
We used our own implementation of the first method of Ina [ 32] here, as we needed a tool for very long alignments (~ 3·106 bp), whereas Xing and Lee [ 21, 29] used a maximum likelihood method implemented in the PAML package [ 33].
SW# is slower only for very long alignments on single GPU card.
Unlike maximum likelihood methods, it afforded considerable results for very long alignments (~ 3·106 bp) and it proved to be fast enough to allow bootstrap resampling.
Furthermore, it is yet unknown which of these methods can scale up to very long alignments, up to hundreds of millions of sites.
Unlike maximum likelihood methods, this was effective for very long alignments (~3*106 bp), and was fast enough to allow bootstrap resampling.
Indeed the average length of CSTs detected by CSTminer is 190 bases, while blastz tries to extend matches to find large synteny tracts, often resulting in very long alignments.
Our approach to resolving cetacean phylogeny resulted in a very long DNA sequence alignment with much missing data (see Figure 3), but we feel that this framework is the best way to summarize all of the available character evidence that is relevant to relationships among cetaceans.
While India has long history of serious trouble with neighboring China, it also has a very long history of non-alignment.
Sequences that were suspected to be chimeric, that lacked 5' or 3' ends, or that had a very long deletion (sequence length in the alignment less than 600 bp) were excluded from the phylogenetic analysis.
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