The instrument includes multiple components which need to be run individually to generate a tree and distance matrix for a pairwise analysis. NINJA generates the tree based on the alignment file.
R CMD CHECK
NINJA generates the distance matrix based on the tree file.
This is the actual distance matrix-generator for NINJA.
This component is optional, and is used to generate the tree file. In case the tree file is not specified, NINJA generates the tree based on the input pairwise alignment file.
NINJA is a component of the CDHIST tool-set. CDHIST is an application suite for producing consistent trees. In this case, it is applied to the two independent components of NINJA, and generates a user-defined tree output format, as well as calculates the distance matrix and store the pairwise distance matrix in a disk file.
The tool-set has the following components:
OpenGeography Maps is an application for visualizing global land and ocean distribution of geographical features (land, ocean, and ice), and the earth’s surface elevation data over time. OpenGeography maps is a web-based application with the OpenGIS Geography Markup Language (GML) software technology used to represent and query a variety of data sets. This includes 2D maps, 3D model, and spatial data sets. The OpenGeography project was developed at the University of Minnesota and is funded by the National Oceanic and Atmospheric Administration, U.S. Geological Survey, National Aeronautics and Space Administration, European Union, and the U.S. Census Bureau.
The R-package avesim is developed to evaluate genetic population structure and dispersal potential of aves. It has been developed as a tool to address avesim’s needs for having an easy-to-use and intuitive framework for analyzing a large number of populations. The package contains three main functions (diveRsity. function, avesim. function, and avesSimo. function) which can be used for different purposes such as testing dispersal potential, sampling and data pre-processing, simulation of dispersal trajectories, and estimation of genetic structure. The package also includes three other functions (diveRsity.Function. eea19f52d2
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