Result attributes¶

The following types of result files are generated once all the requested analyses have completed.

Genotype_set_measures.tsv: All phenotype/genotype-set level results are reported in this file.
<genotype-set-name>_genotype_measures: All genotype-level results are reported in this file. The <genotype-set-name> is just a place holder for the name of the genotype-set whose genotypes are being reported. One file is generated per genotype-set.
Genotype_set_overlap.tsv: This file is organized as a symmetric matrix, where the first row and first column constitute names of all genotype sets being analyzed, all diagonal values are NaN, and each of the rest of the cells contains the No. of overlapping genotypes between the two genotype- sets represented by the corresponding row and column headers. The following figure provides an example:

phenotype_network.gml: The analysis_phenotype_network stored in GML format.
<genotype-set-name>.gml: The entire genotype network corresponding to genotype-set-name stored in GML format.
<genotype-set-name>_dominant.gml: The dominant genotype network corresponding to the genotype-set-name stored in GML format.
Epistasis squares: If the input parameter store-epistasis-squares is enabled and epistasis analysis is used, all squares are written to disk. Four files are generated, where each file corresponds to one of the epistasis types, including ‘no epistasis’. Once the analysis is complete, these files are compressed into a zip archive called epistasis_squares.zip. The archive is available in the output directory.

The following sections describe the various output attributes.

Genotype-set-level results¶

Genotype-set-level results are written to Genotype_set_measures.tsv. The following table describes each output attribute. The Attribute column states the name of the column as it appears in Genotype_set_measures.tsv, the Analysis column states the analysis that generates the attribute, and the Description column describes the attribute.

Attribute	Analysis	Type	Description
Genotype_set	Any	str	Name of the genotype set
Robustness	Robustness	float	Average robustness value computed for the genotype set.
Evolvability	Evolvability	float	Phenotype evolvability value computed for the genotype set.
Evolvability_targets	Evolvability	list	List of genotype sets accessible from this genotype set by a single mutation.
Interface_edges	Evolvability	dict	Counts for all possible types of external mutations. Each key in the dict is a genotype set name with another dict as the value. Keys for the nested dicts are mutation types with the corresponding counts as values.
Accessibility	Accessibility	float	Accessibility value computed for the genotype set.
Neighbor_abundance	Neighbor Abundance	float	Neighbor abundance value computed for the genotype set.
Diversity_index	Diversity Index	float	Diversity index value computed for the genotype set.
Number_of_peaks	Peaks	int	No. of peaks detected in the fitness landscape.
Peaks	Peaks	dict	Each key in the dict is an integral id assigned to a peak, and the corresponding value is a list of all genotypes that lie in this peak.
Number_of_squares	Epistasis	int	No. of squares found during epistasis analysis.
Number_of_squares	Epistasis	int	Total No. of squares found during epistasis analysis.
Magnitude_epistasis	Epistasis	float	Ratio of the number of squares characterized by magnitude epistasis, to the total number of squares in the genotype network.
Simple_sign_epistasis	Epistasis	float	Ratio of the number of squares characterized by simple sign epistasis, to the total number of squares in the genotype network.
Reciprocal_sign_epistasis	Epistasis	float	Ratio of the number of squares characterized by reciprocal sign epistasis, to the total number of squares in the genotype network.
Summit	Peaks	list	A list of all genotypes with highest Score value.
Ratio_of_accessible_mutational_paths	Paths	dict	Each key in the dict is a path length, and the corresponding value is the ratio of accessible mutational paths of this length, to the total No. of paths of this length in the network.
Ratio_of_overlapping_genotype_sets	Overlap	float	Ratio of the number of overlapping genotype sets to the total number of genotype sets under consideration.
Overlapping_genotype_sets	Overlap	list	List of names of genotype sets, where each genotype set has at least one genotype in common with this genotype set.
Number_of_genotype_networks	Structure	int	Number of connected components, i.e., number of genotype networks within the genotype set.
Genotype_network_sizes	Structure	list	List of sizes of all genotype networks, i.e., connected components, within the genotype set.
Size_of_dominant_genotype_network	Structure	int	Size of the dominant genotype network, i.e., the giant component.
Proportional_size_of_dominant_genotype_network	Structure	float	Ratio of the No. of genotypes in the dominant network, to the total No. of genotypes in the entire genotype set.
Edge_density	Structure	float	Edge density of the genotype network.
Average_clustering_coefficient_of_dominant_genotype_network	Structure	float	Average clustering coefficient computed for the dominant genotype network.
Assortativity	Structure	float	Assortativity of the the genotype network.

Genotype-level results¶

Genotype-level results are written to <gentype-set-name>_set_measures.tsv. The following table describes each output attribute. The Attribute column states the name of the column as it appears in <gentype-set-name>_set_measures.tsv, the Analysis column states the analysis that generates the attribute, and the Description column describes the attribute.

Attribute	Analysis	Type	Description
Sequence	Any	str	The genotype.
Robustness	Robustness	float	Genotype robustness.
Evolvability	Evolvability	float	Genotype evolvability.
Evolvability_targets	Evolvability	dict	Each key is the genotype-set name, and value is a list of genotypes in the genotype set to which the focal genotype can evolve.
Evolves_to_genotypes_in	Evolvability	list	List of names of the genotype sets to which this genotype can evolve.
Overlaps_with_genotypes_in	Overlap	list	List of names of the genotype sets which also contain this genotype.
Shortest_path_length	Paths	int	Length of the shortest path from this genotype to the summit.
Shortest_accessible_path_length	Paths	int	Length of the shortest accessible path from this genotype to the summit.
Accessible_paths_from	Paths	int	No. of accessible mutational paths from this genotype to the summit.
Coreness	Structure	float	Coreness is an alternative measure of mutational robustness.
Clustering_coefficient	Structure	float	The clustering coefficient measures the proportion of a vertex’s neighbors that are neighbors themselves.