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Cysteine-rich proteins were excluded from the phylogenomic analysis, since they were found to be problematic to align probably due to their frequent possession of highly repetitive sequences.
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From the perspective of land plant alignments, matK is also problematic, as it was difficult to align seed plants with other land plants (e.g., the seed plant alignment took about two person days to complete and carefully check for the current small sample of taxa).
Problematic sequences that are difficult to align or result in extraordinarily long branches were excluded from the individual unmasked alignments and all single protein datasets were re-aligned with MAFFT and masked using ALISCORE.
Although alignment algorithms can be used to accurately determine the location of any sequence, it is more problematic to determine whether a variation that is identified in an aligned sequence is a true genetic variation.
"Schoenberg is not problematic to me".
Remarriages aren't particularly problematic to represent.
It is problematic to standardise products not fully developed.'.
"And that's really problematic to me".
This view seems problematic to me.
It was problematic to say the least.
(3) The organization of most eukaryotic genomes makes it problematic to identify pseudogenes and their corresponding orthologs, so we focused instead on other classes of noncoding regions, that is, introns or intergenic regions that can be readily aligned among species.
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