The phrase "alignment software to" is correct and usable in written English.
It can be used when referring to software that is designed for aligning or adjusting something, typically in a technical or engineering context.
Example: "We need to install the alignment software to ensure that all components are properly calibrated."
Alternatives: "alignment tools for" or "software for alignment of".
Simulated detector data was used as input for the Millipede-II alignment software to recover the applied misalignments, which was accurately possible.
We have developed CYNTENATOR, a progressive gene order alignment software, to identify genomic regions of conserved synteny over a large set of diverging species.
Thus, there is no requirement to select, a priori, a subset of genomes that is suspected of harboring informative relationships, as is the case when utilizing whole genome alignment software to approach this problem.
For instance, consider a situation that happens regularly with each release of a new reference genome for resequencing, or with the update of sequence alignment software: to ensure that analysis results stay relevant, such events require that the full set of experimental results (e.g. single nucleotide polymorphism discovery) be reevaluated from scratch using the new model data or software.
Typically, failure to detect genetic variants in NGS data is a result of the inability of the alignment software to map the sequenced variant reads to the genomic region, or a failure to sample the variant allele sufficiently or at all [ 1].
We have also used the AceView alignment software[ 18] to co-align these 3.6 million reads for A and B samples to the human genome to identify over 20,000 new exon junctions in the human transcriptome.
Comparisons of operational taxonomic units (OTUs) based on V9 domains and (almost) complete SSU rRNA sequences are almost impossible on large data sets of sequences because none of the multiple sequence alignment software is able to properly align SSU rRNA sequences within their divergent domains, and this problem is exacerbated for short divergent tag sequences (Guillou & Christen unpublished).
Proper selection of the input parameters for the alignment software is essential to obtain optimum alignment results in chromatographic profiling experiments.
We then analyzed the Aeadsx genomic sequence, including the two female-specific exons 5a and 5b and the surrounding intron regions, using the MACAW alignment software [ 52] to identify putative Drosophila, lepidopteran and hymenopteran cis-acting elements potentially involved in splicing regulation of Aeadsx.
Read pairs were checked for a possible normal match to the reference genome using BLAT [ 32], since the alignment software sometimes aligns a read to an homologous sequence instead of its true match, perhaps because of sequencing errors or polymorphisms.
Second, since ELAND alignment software allows 2 mismatches to map any read, we wanted to make sure that sequencing errors would not influence mapping.
