Reverse ecology analysis software tools | Population genetics data analysis
Reverse ecology has been developed to study the complex interactions and species composition of microbial communities. Reverse ecology uses genomics to study community ecology with no a priori assumptions about the organisms under consideration. Researchers can use it to infer the ecology of a system directly from genomic information. The reverse ecology framework uses advances in systems biology and genomic metabolic modeling and the system-level analysis of complex biological networks to predict the ecological traits of poorly studied microorganisms, their interactions with other microorganisms, and the ecology of microbial communities. Several studies have applied this approach to investigate the interactions between microorganisms and their surroundings on a large scale.
Supplies a set of methods for community ecologists. vegan is an R package which consists in three main parts: (i) ordination methods such as detrended correspondence or redundancy analysis; (ii) features dedicated to the manipulation of distance matrices including ANOSIM and Mantel tests; and (iii) several utilities to uniformize data as well as a module allowing users to read Cornell Ecology Program file format.
Provides a virtual portal that allows researchers to run multiple workflows. BioVel supplies a laboratory that gathers functionalities for supporting complex data biodiversity science and ecology research. It proposes workflow assortments in taxonomic refinement, ecological niche modeling, metagenomics, phylogenetics, population modeling, and ecosystem modeling which can be directly run or downloaded.
Identifies multiple subsets that meet the minimum nearest neighbor distance (NND) constraint. spThin is a spatial method that takes a set of occurrence records. It provides a spatial thinning method, which can be used to process occurrence records for use in constructing and evaluating ecological niche modeling (ENMs), as well as in other spatial analyses. It also enables research into the optimal level of thinning for various species in varying environments.
A web tool for analyzing the topology of metabolic networks and calculating the set of exogenously acquired compounds. NetSeed is based on the seed detection algorithm, that allows for the quantification of an organism's metabolic dependence on its environment and enables the transformation of high-throughput genomic data into large-scale ecological data.
Allows development of ecological niche models (ENM) using Maxent. kuenm automates important calibration and evaluation steps in ENM. This tool permits researchers to test distinct sets of environmental variables, which can be used to test hypothesis of variable contribution, or to test among distinct calibration areas.
An R package and a Shiny Web application that implements the reverse ecology algorithm for determining microbe–microbe interactions in microbial communities. RevEcoR allows users to obtain large-scale ecological insights into species’ ecology directly from high-throughput metagenomic data. The software has great potential for facilitating the study of microbiomes.
Allows characterization of human-associated bacterial and phage communities by their inferred relationships. This network-based approach provides a basic understanding of the network dynamics associated with phage and bacterial communities on and in the human body.