The phrase "alignment but also in" is not correct and lacks clarity in written English.
It may be used in contexts where you are discussing multiple aspects of alignment, but it needs additional context to be meaningful.
Example: "The project requires alignment but also in terms of team dynamics."
Alternatives: "alignment as well as in" or "alignment and also in".
The results can be examined in detail not only in the alignment or histogram viewer but also in the track viewer (Supplementary Figs S1A and S3).
BLAST shows not only identical amino acids at a given position in the alignment, but also homologous substitutions, which are determined from the scoring matrix.
The alignment shown in Figure 3 also serves to highlight two sequence motifs that are conserved among deuterostomes but also in a mosaic of protostomes and unicellular eukaryotes (QLDL449-452 and FRDY).
Here, tetrapod exons 17 to 21V22 align with the teleost repeats such that the sequence alignment results also in an alignment of the secondary structure elements, i.e., the beta strands.
The multiple sequence alignments were performed with the ClustalW multiple alignment application also in BioEdit version 7.1.3.
This maximizes the amount of sequence information that we use in the alignment, but it also favors the inclusion of sequences that contain low frequency and/or species-specific exons, potentially increasing the number of alignment errors.
However, the fact that we recently discovered a phylogenetic pattern similar to that from the first part of the XY1 alignment also in the RPD2b gene (unpublished data) can be interpreted as support for the hybridization/introgression hypothesis.
SHRiMP and SHRiMP2 are parallel alignment tools, available also in a distributed version [ 16], implemented upon the MapReduce programming model [ 17].
The correctly folded secondary structure is fundamental not only for improving the alignment [ 43- 48], but also for building the alignment itself (especially in case of variable markers such as ITS2) as well as for identifying and detecting synapomorphies.
Next, the CAGE software [ 19] uses a combinatorial approach to identify all pairwise orthologs in the alignment data, according to the definition of orthology in [ 22, 23]; its output is a subset of the inter-species alignments, also in MAF format.
