Sentence examples for truncated alignment from inspiring English sources

Trimming the amino acid alignment of ambiguously aligned regions resulted in a truncated alignment of 592 characters, with most trimmed regions in Domain I and the interdomain region between Domain I and Domain III.

This truncated alignment was transformed into its DNA coding version (Additional file 1), which was used to generate a phylogenetic tree by PhyML (Fig. 2).

This manually truncated alignment, consisting of 218 residues, was used to determine the phylogenetic relationship between the A. gambiae GSTs by both distance and parsimony methods.

Evolutionary distances were estimated using the distance matrix created by the PROTDIST program of PHYLIP package [ 33] based on a truncated alignment of AANATs and using the Jones-Taylor-Thornton (JTT) substitution model [ 23].

A representative distance tree, derived from the N-terminal truncated alignment is shown in Figure 2. The two largest GST classes in A. gambiae are the insect specific delta and epsilon classes with 12 and 8 members respectively.

Truncated alignments were input to PhyML for phylogenetic analysis using the parameters described above.

Final truncated alignments consisted of 268 and 208 sequences of 614 and 319 nucleotides in length, for COI and EF1a, respectively.

If not noted otherwise, identities are reported for the whole alignments i based on truncated alignments Thirty-six (53.7 %) of the reconstructed genes are homologous to previously functionally characterized genes of WSSV (and other organisms in the case of IAP.

Robustness of root positioning was evaluated with two truncated alignments, one with the LDH and 'LDH-like' MDH sequences removed and the other with the cytosolic and mitochondrial MDH sequences removed.

Examining the objective function (10) we see that we can also set ϕ n m to zero for these truncated alignments (using the convention that 0 ln (0 ) = 0 ) and thus also γ n m = − ∞ for the same.

Truncated opsin alignment used for phylogenetic analyses and ML and Bayesian tree files were uploaded on the DRYAD repository (http://www.datadryad.org) [ 118– 118].