Sentence examples for alignment was constructed with from inspiring English sources

Multiple alignment was constructed with CLUSTALW [26].

Multiple sequence alignment was constructed with the Clustal×program [40].

This alignment was constructed with preservation of the Lnx3 reading frame (all the deletions/insertions causing frameshift were discharged from the alignment).

The alignment was constructed with PROMALS3D (http://prodata.swmed.edu/promals3d ).edu/promals3d

A multiple sequence alignment was constructed with BioEdit (version 7.0).

env sequence alignment was constructed with translated amino acid sequences using Muscle v3.8.31 [ 30].

The alignment is constructed with PRANK (Loytynoja and Goldman 2008) and edited manually to removed small gappy regions at the end tails of some of the mitochondrial protein genes.

Protein alignments were constructed with MAFFT [ 131], and poorly aligned regions were removed with Gblocks [ 132].

Full-length protein alignments were constructed with MUSCLE and were curated by removal of poorly aligned positions using GBlocks (using the lowest stringency parameters), excepting for the Oxa protein phylogeny where only gap positions were removed in order to retain a sufficiently large data set.

The multiple sequence alignments were constructed with ClustalW2 [61] together with Saccharomyces sequences and orthology mappings obtained elsewhere [46], [62].

Duplicates and incomplete proteins were removed, and multiple alignments were constructed with the CLUSTALX program [60] and an initial phylogenetic tree was created using the MEGA 4 package.