Sentence examples for the underlying alignment from inspiring English sources

Fourth, SiPhy, like other existing methods, heavily depends on the underlying alignment.

The underlying alignment method computes alignments with a worst-case bound on their quality.

Such methods heavily depend on the sequence conservation and quality of the underlying alignment.

The underlying alignment scoring scheme is the general reversible model [ 21]: where Q is the transition rate matrix.

We show that this instability is due to instabilities of the underlying alignment procedures that are, in turn, caused by sequence repeats.

Since a phylogenetic tree is only as good as the underlying alignment, splitting the kinases into families prior to generating phylogenies is a more powerful method for comparing entire kinomes.

The network topology in Fig. 6A and 6B indicates that the ECH domain in the archaeal bifunctional proteins is more similar to the sECH ECH domain than either of these two domains is to the ECH in the other bifunctional protein cluster; a look at the underlying alignments indicates that the domain ordering between archaeal and non-archaeal bECH sequences has been reversed (Fig. 5D, Fig. 6C).

In all these applications, the reliability and accuracy of the analyses depend critically on the quality of the underlying alignments.

To investigate the reasons for the occurrence of these rather distinct tree topologies, we analysed the underlying alignments.

This showed clearly that the instabilities and inconsistencies of the safe branches can be traced back to the underlying alignments.

In view of their rather restrictive definition, it was natural to guess that that instabilities of safe branches indicate instabilities of the underlying alignments.