Monthly Archives: January 2012

Genepop

General information 4.1 version. Genepop is a population genetics software package, which has options for the following analysis: Hardy Weinberg equilibrium, Linkage Disequilibrium, Population Differentiation, Effective number of migrants, Fst or other correlations. How to use To execute Genepop in … Continue reading

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CLUMPP

General information 1.1.3 version. CLUMPP is a program that deals with label switching and multimodality problems in population-genetic cluster analyses. CLUMPP permutes the clusters output by independent runs of clustering programs such as , so that they match up as … Continue reading

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Structure

General information 2.33 version. The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and … Continue reading

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MCCCS Towhee 7.0.2

Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been … Continue reading

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Gulp 4.0

General Information GULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids). The focus of the … Continue reading

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LAMMPS

LAMMPS (“Large-scale Atomic/Molecular Massively Parallel Simulator”) is a molecular dynamics program from Sandia National Laboratories. LAMMPS makes use of MPI for parallel communication and is a free open-source code, distributed under the terms of the GNU General Public License. LAMMPS … Continue reading

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Arina cluster

General information Summary Arina has 3.728 cores distributed in 3.664 xeon cores, and 64 Itanium2 cores with RAM memory ranging from 16 to 512 GB per node. Four of the xeon nodes have 2 Nvidia Tesla cards each, another node with  two Nvidia … Continue reading

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