The phrase "alignment to construct a" is correct and usable in written English.
It can be used in contexts where you are discussing the process of aligning elements or ideas to create something.
Example: "The team focused on alignment to construct a cohesive strategy for the project."
Alternatives: "coordination to build a" or "congruence to develop a".
We used this core genome alignment to construct a maximum likelihood phylogeny of the 89 K.
To find more ancient relatives of UlaG among MBL RNases, we used a structure-guided sequence alignment to construct a profile Hidden Markov (HMM) model [ 33] to probe the complete non-redundant protein sequence database.
Since different multiple alignment software packages can yield very different alignments, use of the profile HMM approach is more robust than relying on a single multiple alignment to construct a consensus or a position-specific score matrix.
Lienau et al. [ 14] combined evidence from protein phylogenetic data and gene presence/absence information into a "mega-matrix", analogous to a large multiple sequence alignment, to construct a parsimony tree which was claimed to be similar to that of [ 8].
In addition to comparing and contrasting the four UPF0201 protein structures, we have used structure based sequence alignments to construct a phylogenetic tree that relates UPF0201 family members to L5 ribosomal subunits and other structurally similar RNA binding proteins, thereby extending the evolutionary purview of the RRM motif superfamily.
We performed a multiple sequence-alignment to construct a phylogenetic tree on the basis of NDBs of the 51 silkworm ABC transporters.
We utilized a second phylogenetic approach, gene alignment concatenation, to construct a species tree.
The 16S rRNA alignment served to construct a reference tree by maximum-likelihood (ML) using TREE-PUZZLE with a HKY nucleotide evolution model [ 48] and a Gamma model [ 49] for evolution rate variation between sites.
The amino acid sequences were aligned using ClustalW and the alignment was used to construct a phylogenetic tree using the neighbor-joining method with MEGA5 version 5.2.2 (http://www.megasoftware.net/) [ 19].
The alignments were then concatenated and the resulting long alignment was used to construct a phylogenetic tree.
This recombinant-free alignment, which had 13,015 less polymorphic sites than the full alignment, was used to construct a new core phylogeny (fig. 2 B).
