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APE / Analyses of Phylogenetics and Evolution
A package for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis. It focuses on statistical analyses using phylogenetic and genealogical trees as input. APE provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. It also produces complex population genetics plots, such as the generalized skyline plot.
Permits to study adaptive evolution using multi-optima Ornstein-Uhlenbeck (OU) models. bayou incorporates different methods into a flexible software package for the R statistical environment. It also provides a reversible-jump algorithm that jointly estimates the location, number, and magnitude of shifts in adaptive optima from phylogenetic comparative data. These scripts can be used to compare specific hypotheses. Furthermore, informative priors can be incorporated from different data sources to test mechanistic interpretations of phylogenetic patterns of trait divergence.
A package for phylogenetic reconstruction and analysis. Phangorn offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation. Extending the general ML framework, it provides the possibility of estimating mixture and partition models. Furthermore, phangorn offers several functions for comparing trees, phylogenetic models or splits, simulating character data and performing congruence analyses.
A software for the analysis of phylogenetic community structure and character evolution. Phylocom calculates numerous metrics of phylogenetic community structure and trait similarity within communities. Hypothesis testing is implemented using several null models. Within the same framework, it measures phylogenetic signal and correlated evolution for species traits. A range of utility functions allow community and phylogenetic data manipulation, tree and trait generation, and integration into scientific workflows.
Phytools / Phylogenetic Tools for comparative biology
A multifunctional phylogenetics package. Phytools implements a number of methods for phylogenetic comparative biology, phylogeny inference, tree manipulation and graphing. Its functionality is concentrated in the phylogenetic analysis of comparative data from species. For example, the package includes functions for Bayesian and ML (maximum likelihood) ancestral state estimation; visual simulation of trait evolution; fitting models of trait evolution with multiple Brownian rates and correlations; visualizing discrete and continuous character evolution using colors or projections into trait space; identifying the location of a change in the rate of character evolution on the tree, etc.
A package which implements a series of methods for detecting associations between species traits and rates of speciation and/or extinction, given a phylogeny and trait data, including the BiSSE (binary state speciation and extinction) method. Diversitree is open source and designed to be fairly straightforward to extend. In particular, any model that can be expressed by moving down a tree (post-order traversal, or ‘pruning’) can be implemented using only a modest number of lines of R code. To facilitate the development of related methods, there is a ‘writing diversitree extensions’ manual available from the diversitree website.
A data-driven phylogenetic comparative method for fitting stabilizing selection models to continuous trait data, building on the ouch package. SURFACE consists of a ‘forward’ stepwise phase in which selective regimes are added to the tree, followed by a ‘backward’ phase that identifies cases where the same regime is reached by multiple lineages. This results in an estimate of the macroevolutionary adaptive landscape that includes measures of the extent of phenotypic convergence. Many clades have long been understood to contain extensive convergence, but statistically appropriate methods for testing the extent of convergence have been lacking. SURFACE allows reassessment of such data sets, and can be used to test whether convergence is greater than expected by chance. As an objective tool for characterizing the macroevolutionary adaptive landscape of a clade, it provides opportunities to understand the dynamics of adaptive radiation.
PHYSIG / Phylogenetic Signal
A Matlab code for the phylogenetic analysis of comparative data using Generalized Least Squares and computer-intensive methods. Physig will perform the randomization test for phylogenetic signal and also calculate the K statistic to gauge how much phylogenetic signal is present. It tests for statistical significance of phylogenetic signal (tendency for related species to resemble each other) by randomization procedure, computes K statistic, which indicates amount of phylogenetic signal relative to expectation under Brownian motion character evolution along the specified phylogenetic tree (topology plus branch lengths. Physig also computes other MSE statistics.
QueTAL / Que Transcription Activator-Like
Offers tailored tools for comparison of Transcripton Activation-Like (TAL) effector genes to infer functional and evolutionary relationships. This toolkit contains two packages, DisTAL for distance calculating with repeated bases and Functal used to calculate distance thanks to DNA binding specificities. QueTAL analysis can rapidly study any TAL effector genes of interest and compare them to other available TAL genes. It also can classify groups of TAL effectors with similar DNA-binding specificities (targeting the same EBEs) or highlighting cases of functional convergence on key susceptibility genes.
A package with which researchers can use the Wheatsheaf index to analyze convergent evolution. Windex allows implementation of this method (the Wheatsheaf index) with additional functions that can be used to create plots and perform statistical tests. It has three main functions. The first, plot.trait, gives a visual representation of the data although the plot does not account for phylogeny and so is only intended for visual data exploration. The second, windex, is the core function of the package. This takes a phylogenetic tree of class ’phylo’ and a dataset and calculates the Wheatsheaf index of convergent evolution along with jackknived 95% confidence intervals. The third function, test.windex, runs the windex function but also performs bootstrapped randomisations of the tips in the tree to generate a null distribution. This distribution is then used to test whether the calculated value of the Wheatsheaf index represents stronger convergence that is expected given the topological constraints of the tree.
PHYREG / Phylogenetic Regression
A tool that implements the phylogenetic regression of Grafen. Phyreg provides general linear model facilities (single y-variable, multiple x-variables with arbitrary mixture of continuous and categorical and arbitrary interactions) for cross-species data. The theory aims to cope with both recognised phylogeny (closely related species tend to be similar) and unrecognised phylogeny (a polytomy usually indicates ignorance about the true sequence of binary splits).
Provides resource for data analysis, data management, and graphics. Stata is an integrated statistical software package where all analyses can be reproduced and documented for publication and review. User can combine and reshape datasets, manage variables, and collect statistics across groups or replicates. It also has advanced tools for managing specialized data such as survival/duration data, time-series data, panel/longitudinal data, multilevel data, categorical data, multiple-imputation data, and survey data.
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