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However, pair-HMMs also have a number of shortcomings, which may negatively affect their alignment performance or make them impractical for certain alignment tasks.
However, despite these advantages, pair-HMMs also have a number of practical limitations that may degrade their alignment performance or render them unsuitable for certain alignment tasks.
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While looking for an optimal alignment, the algorithm looks for certain constrained alignments based on what they call a hierarchical constraint.
It takes a certain alignment of political and geographical factors to give birth to a tradition like this one.
In alignment masking, certain alignment columns and input sequences are excluded from phylogenetic analysis.
This step is important because some of the classes require you to be of a certain alignment, or have certain restrictions on which alignments you can be.
The BLAST-based alignment method produces better separation for certain taxonomy groups than the global alignment method does.
However, it is impossible to know for certain if all positions in an alignment are assigned correctly even when using state-of-the-art methods.
Secondary structures for resulting clades were established for certain representatives of the clade by aligning to known structures from the European RNA Database [ 18, 33] in separate alignments for each clade and considering compensatory base changes.
Missing sequences for certain taxa in certain partitions were coded as missing data in the respective alignments.
Although all three designs are fairly tolerant to misalignments in the studied range, square electrodes show the highest sensitivity to alignment errors and show a reduction of the holding force that reaches 16% for certain planes in the trap.
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