Genotype networks are a concept used in systems biology to study sets of genotypes having the same phenotype, and the ability of these to bring forth novel phenotypes. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of systems such as metabolic networks and RNA folds.
Automatically assigns K numbers to genes in the genome, enabling reconstruction of KEGG pathways and BRITE hierarchies. The method is based on sequence similarities, bi-directional best hit information and some heuristics, and has achieved a high degree of accuracy when compared with the manually curated KEGG GENES database.
Genotype networks are a representation of the set of genotypes associated with a single phenotype, and they allow one to estimate properties such as the robustness of the phenotype to mutations, and the ability of its associated genotypes to evolve new adaptations. So far, though, genotype networks analysis has rarely been applied to population genetics data. To help fill this gap, VCF2Networks is a tool to determine and study genotype network structure from single-nucleotide variant data.
Analyses and visualizes genotype networks. The Genonets Server provides the following features: (i) the construction of genotype networks for categorical and univariate phenotypes from DNA, RNA, amino acid or binary sequences; (ii) analyses of genotype network topology and how it relates to robustness and evolvability, as well as analyses of genotype network topography and how it relates to the navigability of a genotype network via mutation and natural selection; (iii) multiple interactive visualizations.
Allows exploration of small genotype-based fitness landscapes, typically less than 10 loci. MAGELLAN is a web-based tool that creates a visual representation which can be dynamically rotated or tuned by several options, and computes the summary statistics that characterizes it. The software can be used to explore model and experimental fitness landscapes.
Furnishes a method for analyzing additive main effects and multiplicative interaction. AMMISOFT can be applied to genotypes-byenvironments treatment design. It can serve for performing different steps: (i) analysis of variance, (ii) model diagnosis, (iii) mega-environment delineation, and (iv) agricultural recommendations.