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Each Nexus file was concatenated manually into a combined executable Nexus file and analyzed under parsimony in a heuristic search implementing 500 random sequence additions saving 100 trees per replicate.
The experiment was set up with four levels (search algorithms): a random search, a search implementing the hill climbing technique, a search implementing the Nelder-Mead method, and a search implementing the proposed adaptive GA.
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The MCS search implemented in SMSD incorporates chemical knowledge (atom type match with bond sensitive and insensitive information) while searching molecular similarity.
The first tabu search procedure (hereinafter called ST or standard tabu search) implements the main features of the TABUROUTE algorithm introduced by Gendrau et al. [11].
Examples of systematic search include exhaustive search implemented in Glide (Friesner et al. 2004), and a fragmentation method named incremental construction algorithm implemented in LUDI (Bohm 1992) and DOCK (DesJarlais et al. 1986).
The phonetic search implemented alongside the search based on the lexicon words allows to find even the words outside the ASR system lexicon such as names, geographic locations or Jewish slang.
This search, implemented in a novel reassortment discovery program, exhaustively enumerates all HA-NA tree incompatibilities that have sufficient statistical support to be considered likely reassortments despite the ambiguities in phylogenetic reconstruction.
The Phytozome BLAST search implements NCBI Blast (v2.2.13).
Also the Phyml search implemented in jModelTest is not the most thorough.
Parsimony analysis was performed by an exhaustive search implemented by the PAUP software package version 4.0b10 [ 102].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com