A one-alignment-one-tree approach may fail to recover an otherwise supported relationship unless the bipartition tables are investigated, because it is not represented in the inferred tree.
The number of differences when a sequence of words is treated as a single name in one alignment and a modifier and a name in another alignment could maybe have been fewer with a slightly modified study.
We represent one alignment A between two proteins as a sequence of alignment states, where L is the alignment length and is the alignment state at position i.
Note that consistency is ensured since, for each sequence S i ∈ A, we have G(S i ) ∈ D as one alignment in A (D ) must contain S i G (S i ).
Combining Equation (1 3), the potential of one alignment A can be calculated as follows.
It is not uncommon for there to be more than one alignment between a query and a coding region.
Each alignment was visually inspected, and one alignment with a pairwise identity below 40% was discarded.
BWA-SW might report more than one alignment for a single read (in rare cases for not very long reads), where one alignment corresponds to one fragment of the read.
TopHat allows Bowtie to report more than one alignment for a read (default=10), and suppresses all alignments for reads that have more than this number.
When there is more than one alignment to a coding region, only the lowest E-value alignment between a particular query and the coding region is used when computing ROC scores.
For each gene family, the alignment with the highest norMD score was used and where more than one alignment had an equal top score the alignment method was chosen at random.
