The phrase "alignment software" is correct and usable in written English.
It can be used when referring to software designed to align or adjust various elements, often in contexts like engineering, design, or data processing.
Example: "The new alignment software significantly improved the accuracy of our measurements in the project."
Alternatives: "calibration software" or "synchronization software".
Based on maximum identity score and query coverage, the best highly identical 10 sequences were selected and aligned using multiple alignment software program, ClustalW (MEGA tool).
PCR products were sequenced by de-deoxy sequencing and sequences were aligned using Multi-Align [37], a multiple sequence alignment software available online (http://bioinfo.genotoul.fr/multalin/multalin.html).html
The two sequenced genomes were aligned using the genome alignment software progressiveMauve [ 66], using default options.
All data sets were aligned with the RNA SALSA alignment software [ 30], considering rRNA secondary structures.
All sequences were aligned using Muscle, a multiple alignment software for protein and nucleotide sequences which allows multiple sequence comparison by log-expectation [38].
The extracted sequence reads were then aligned with reference sequences by Cap3 alignment software (http://seq.cs.iastate.edu/).edu/
COI and 28S sequences were aligned using the web interface of the multiple alignment software MAFFT ([33]; available at http://www.ebi.ac.uk/Tools/mafft/index.html), under default settings.
Rolexa reads were therefore aligned to the reference genomic sequence using the global alignment software align0 using the method described hereafter.
To do so, we align the related domains with the MUSCLE (Edgar, 2004) alignment software.
The resulting reads were aligned to the reference mouse genome (mm10) using Bismark alignment software (version 0.10.0) [ 71].
Nucleotide sequences of 24 teleost V1r sequences and mouse V1rb2, V1re4 and V1rf3 were aligned using ClustalX [32] and manually rearranged using the Bioedit alignment software (v. 7.0.5.3).
