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The mothur package of algorithms (v1.32.1) was used for analysis [ 7].
We used the Sawyers test in the Geneconv package of algorithms for these minor clades analyses.
The MOTHUR package of algorithms (v1.30) was used for analysis [ 19].
DNA polymorphism analysis and recombination analysis were performed with the DNasp package of algorithms http://www.ub.es/dnasp.ub.es/dnasp
Alignments were also created with the DNasp package of algorithms (www.ub.es/dnasp) to calculate mean nucleotide diversity per aligned base.
Thus, the next critical field for improvement in GBS is likely to be an imputation algorithm or package of algorithms that can answer its unique requirements.
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We thank all major contributers to earlier versions of the ViennaRNA Package whose implementation of algorithms and programs helped to create this versatile and comprehensive software collection (in alphabetical order): Wolfgang Beyer, Sebastian Bonhöffer, Martin Fekete, Walter Fontana, Ulrike Mückstein, Wolfgang Schnabel, Manfred Tacker, and Stefan Wuchty.
Constraint-based protein structure prediction (CPSP) tools is a package of very fast algorithms for ab initio optimal structure prediction and related problems in 3D HP-models [cubic and face centered cubic (FCC)].
DaliLite is a standalone package of the Dali algorithm.
Other R packages are specializing on particular set of algorithms, for instance the R package tree focuses on producing classification and regression trees.
A number of algorithms and software packages, which may be wrapped as SADI services, require the specification of one or more parameters.
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