The phrase "alignment for which" is correct and usable in written English.
It can be used when discussing a specific alignment related to a particular context or criteria.
Example: "The alignment for which we are aiming is crucial for the success of the project."
Alternatives: "alignment that" or "alignment pertaining to".
Our approach starts with assembly-versus-assembly alignment, for which we use the LAST aligner [ 16] with the application of a split-alignment algorithm (Martin Frith, personal communication).
We name "work positions" positions in the multiple alignment for which at least 8 amino acids are aligned.
In this case we consider as correct an alignment where the current range image is attached correctly to an existing cluster (that is, we consider as erroneous only the alignment for which a new cluster is created, rather than all the other images which may attach to it correctly).
Thus, columns in the alignment for which "positional homology" cannot be robustly determined must be excluded from subsequent analyses.
Columns in the alignment for which a gap was present in >10% of the sequences were removed.
The different multiple alignments were concatenated into one large alignment for which a distance matrix was calculated based on Poisson correction using the software package TREECON [ 34].
Fifth, sequences were collapsed based on ungapped alignments for which neither sequence was required to be fully aligned.
This optimization was carried out by generating all possible ungapped alignments, for which a score is assigned according to the quality of their corresponding models.
We built the genetic-similarity tree using PHYML from a set of sequences consisting of positions in the locus alignments for which at least two sequences differed from the consensus.
