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Exact(2)
At the end of the video, the path identifier held by the token with the minimum alignment cost allows the best event sequence to be traced back and the corresponding boundaries recovered.
Denote by HSA T, S) the minimum alignment cost of an HSA between T and S, and call an HSA A optimal with respect to T and S if w(T, S, A) = HSA T, S).
Similar(58)
The minimum alignment count per locus was set to 20 (-c option).
Compute all of the minimum pairwise alignment costs c ij using dynamic programming.
¥ Lowest common ancestor (LCA) using 1e-5 cutoff, 60% minimum identity, and a minimum alignment lenght cutoff of 15.
This search identified 708 hits (E<e−10, identity ≥ 70%, and minimum alignment length >50 bp).
Minimum alignment length coverage (-L parameter) varied between 0.1 and 0.9 with step size 0.1.
† = maximum e-value of 1x10-5, minimum alignment length ~100.
The minimum alignment score was set at 150.
A minimum alignment length l A,min of 20 nt is used for finding pairwise alignments.
Individual alignments were parsed by minimum alignment length and concatenated using FasConcat [ 75] for generation of super alignments.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com