The split between the freshwater clades (Cambaridae, Astacidae, Parastacidae) and the Nephropidae is most prominent in this alignment.
The improvement was most prominent when there was alignment ambiguity in functional regions due to binding sites that were not highly conserved.
The most prominent feature of the resulting alignment is the presence of several highly conserved blocks of amino acids separated by species- and protein-specific insertions.
If none of the databases or algorithms meet your satisfaction consider constructing your own if you have sufficient programming skills in for example BioPerl or BioPython, the two most prominent languages used in constructing the alignments using the defined algorithms.
(PDF 111 kb) Additional file 3: Multiple sequence alignment showed the other 4 most prominent motifs of GRAS domain: LR I, LR II, PFYRE, SAW, respectively.
This problem is particularly important in the field of phylogeny reconstruction, because multiple alignment acts as a preprocessing step in most prominent methods of inferring a phylogenetic tree of sequences.
Distributed alignment tools have also been created, with Crossbow (Langmead et al., 2009a) as one of the most prominent examples.
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