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Compatibility and performance issues among compiler and operating system combinations were assessed for an example case: the Cropping System Model (CSM) as implemented in version 4.5 of the Decision Support System for Agrotechnology Transfer (DSSAT).
Networks were constructed using the Neighbor-net algorithm as implemented in Version 4.11.3 of SplitsTree [ 61].
The approach described by Wolc et al. [ 28] and implemented in version 4.0 of the GenSel software (http://bigs.ansci.iastate.edu/) was used to identify associated windows (i.e. genomic regions).
The following algorithm is implemented in version 2.8 of the freely available tool BIOCHAM, a modeling environment for the analysis of biological systems (Calzone et al., 2006).
Brain gray matter (GM) and white matter (WM) volume was derived from the first segmentation process as implemented in version 5 of the software package Statistical Parametric Mapping (SPM5).
Genotype data and phenotype data from previous studies [ 14, 15, 21] were analyzed to map QTLs using the CIM method [ 40, 41], as implemented in version 2.5 of WinQTL Cartographer [ 42].
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Complete chloroplast sequences were aligned using MAFFT61 version 7.017 implemented in Geneious version 7.1.7 (Biomatters Ltd.).
Sequence alignments were performed by using ClustalX version 1.83 implemented in BioEdit version 7.2.5 (http://www.mbio.ncsu.edu/BioEdit/BioEdit.html).html
For the analysis with Monolix, version 4.3.2 was used, as implemented in MATLAB version 8.1 [ 30].
Sequence and alignment manipulation was implemented in Perl (version 5.10.1), quantization and analysis in R (version 3.0.0).
Maximum likelihood (ML) analysis implemented in PHYML version 3.0 [ 45] and Bayesian inference (BI) implemented in MrBayes version 3.1.2 [ 46] were used to construct phylogenetic trees.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com