Sentence examples for alignment tree from inspiring English sources

Such models describe the substitution process based on a multiple alignment tree.

The substitution rate for each alignment column was divided by the codeml estimated alignment tree length to control for the mutation rate of the encoding gene.

This is the case for both the manually aligned dataset (Figure S1) where sequences assigned to the Bacteroidetes branch within a clade of Proteobacterial sequences and the Greengenes' NAST alignment tree (Figure S2) where a sequence assigned to cyanobacteria groups within the Firmicutes clade.

HMB carried out nematode extraction and sequencing, sequence alignment, tree building, and drafted the manuscript.

This method uses a joint reconstruction framework that simultaneously infers the alignment, tree, and insertion/deletion rates.

In this 3D alignment tree, the homologs of the superfamily can be clearly separated into four subclusters.

Concatenated alignment trees were generated from the original alignments for the different datasets.

However there are other potential sources of phylogenetic conflict between gene trees and concatenated alignment trees.

Alignment trees were constructed using the Neighbor Joining method with 1000 bootstraps.

An alternative approach views concatenated alignment trees as consensus-like, and focuses on the congruence between such trees and the underlying gene trees [ 41, 42, 44].

After visual inspection of the alignment, trees were reconstructed using PhyML v3.0 with the model determined by ProTest and 100 bootstrap resamplings (Guindon et al. 2010).