Architecture: x86_64
Operating System: SUSE Linux Enterprise Server 11 sp2
Resource manager: Torque 4.1.4
Cluster scheduler: Maui 3.3.1


Packages installed
Package Version Description Install
Abaqus 6.1.3 Engineering simulation software /opt/exp_soft/abaqus/Commands/
admb 11.5 Non-linear statistical modeling /opt/exp_soft/admb-11.5pre
AFNI 2014 Analysis of Functional NeuroImages /opt/exp_soft/AFNI/NIH.openSUSE.11.4_64
Amos 3.1.0 A Modular Open Source Assembler /opt/exp_soft/amos/
AmberTools 14 molecular mechanical force fields for the simulation of biomolecules /opt/exp_soft/AmberTools/amber14
Annovar 5 tool to functionally annotate genetic variants detected from diverse genomes /opt/exp_soft/annovar
Ansys Fluent 15.07 Flow turbulence heat transfer and reaction modeling /opt/exp_soft/ansys-15.07
Argtable 2.13 ANSI C library for parsing GNU style command line options /opt/ext_soft/argtable2-13
bamtools 2.2.3 Command-line toolkit for working with BAM data /opt/ext_soft/bamtools
bamtools 2.4.1 Command-line toolkit for working with BAM data /opt/ext_soft/bamtools-2.4.1
BCFtools 1.2 flexible generic format for storing nucleotide sequence alignment /opt/exp_soft/bcftools-1.2
Beagle 1 high-performance library for Bayesian and Maximum Likelihood phylogenetics packages /opt/exp_soft/beagle-lib
Beagle 2.1.2 high-performance library for Bayesian and Maximum Likelihood phylogenetics packages /opt/exp_soft/beagle-lib-2.1.2
BEAST 1.7.5 Cross-platform program for Bayesian MCMC analysis of molecular sequences /opt/exp_soft/BEASTv1.7.5/bin
BEAST 1.8.0 Cross-platform program for Bayesian MCMC analysis of molecular sequences /opt/exp_soft/BEASTv1.8.0/bin
BEAST 1.8.2 Cross-platform program for Bayesian MCMC analysis of molecular sequences /opt/exp_soft/BEASTv1.8.2/bin
BEAST 2.1.3 Cross-platform program for Bayesian MCMC analysis of molecular sequences /opt/exp_soft/BEASTv2.1.3/bin
BEAST 2.4.7 Cross-platform program for Bayesian MCMC analysis of molecular sequences /opt/exp_soft/BEASTv2.4.7/bin
BLAST 2.2.27 Software for comparing primary biological sequence information /opt/exp_soft/blast-2.2.27/bin
BioPerl 1.6.1 perl modules useful in building bioinformatics solutions /opt/exp_soft/BioPerl-1.6.1
Bowtie 1.0.0 Ultrafast memory-efficient short read aligner for short DNA sequences from next-gen sequencers /opt/exp_soft/bowtie-1.0.0
Bowtie2 2.1.0 Ultrafast memory-efficient short read aligner for short DNA sequences from next-gen sequencers /opt/exp_soft/bowtie2-2.1.0
Bowtie2 2.2.6 Ultrafast memory-efficient short read aligner for short DNA sequences from next-gen sequencers /opt/exp_soft/bowtie2-2.2.6
BWA 0.7.5a Burrows-Wheeler Aligner is a program for aligning sequencing reads against a large reference genome /opt/exp_soft/bwa-0.7.5a
Breseq 0.27.0 breseq is a computational pipeline for finding mutations /opt/exp_soft/breseq/breseq-0.27.0-Linux-x86_64/
C\C++ 4.6.1 GCC C and C++ $PATH depending on module selection
C\C++ 4.8.1 GCC C and C++ $PATH depending on module selection
C\C++ 4.8.4 GCC C/C++/gFortran module load compilers/gcc484
C\C++ 4.9.2 GCC C/C++/gFortran module load compilers/gcc492
C\C++ 5.3.0 GCC C/C++/gFortran module load compilers/gcc530
CasaCore 1 Libraries for radio astronomy /opt/exp_soft/casacore
cdo 1.6.9 Climate and NWP model Data analyzer /opt/exp_soft/cdo-1.6.9
chromopainter 0.0.4 A tool for finding haplotypes in sequence data /opt/exp_soft/chromocombine-0.0.4
ClustalW 2.0.10 General purpose multiple sequence alignment program for DNA or proteins /opt/exp_soft/clustalw/bin
Clustal Omega 1.2.1 Multiple Sequence Alignment /opt/exp_soft/clustal-omega-1.2.1
Crux 1.4x Mass spectrometry analysis and peptide identification (incl bug fix) /opt/exp_soft/crux-1.4x/bin
Crux 2.1 Mass spectrometry analysis and peptide identification (incl bug fix) /opt/exp_soft/crux-2.1/bin
Cufflinks 2.1.1 assembles transcripts estimates their abundances and tests for differential expression and regulation in RNA-Seq samples /opt/exp_soft/cufflinks-2.1.1
DepthMap 0.26 Spatial network analyses /opt/exp_soft/depthmapX
DL_POLY 1.9 Classic General purpose serial and parallel molecular dynamics simulation package /opt/exp_soft/dl_class_1.9
DL_POLY 2.2 General purpose serial and parallel molecular dynamics simulation package /opt/exp_soft/dl_poly_2.20
Eigensoft 6.0.1 Explicit modelling of ancestry differences /opt/exp_soft/EIGENSOFT-6.0.1
Emboss 6.6 Molecular Biology Application /opt/exp_soft/emboss-6.6/bin
FastQC 0.10.1 Quality control application for high throughput sequence data /opt/exp_soft/FastQC
FastQC 0.11.3 Quality control application for high throughput sequence data /opt/exp_soft/fastqc-0.11.3
FASTX-toolkit 0.13.2 Tools for Short-Reads FASTA/FASTQ files preprocessing /opt/exp_soft/fastx-0.13
FFTW 3.2.2 C subroutine library for computing Discrete Fourier Transform $PATH
foamExtend 4.0 Open source CFD software /opt/exp_soft/foam/foam-extend-4.0
Fortran 77 4.6.1 GCC Fortran $PATH depending on module selection
Fortran 95 4.0.3 GCC Fortran /opt/exp_soft/fortran-g95
freebayes 0.9.21 Bayesian haplotype-based polymorphism discovery and genotyping /opt/exp_soft/freebayes
FREESURFER 5.3.0 Automated tools for reconstruction of the brain.s cortical surface from structural MRI data module load freesurfer-5.3
FFP 3.19 Alignment free comparison tool for phylogenetic analysis /opt/exp_soft/ffp-3.19/
Gromacs 4.5.7 GPU aware Molecular dynamics package /opt/exp_soft/gromacs-gpu
Gromacs 4.6.2 Molecular dynamics package /opt/exp_soft/gromacs-mpi
Gromacs 2016.1 Molecular dynamics package /opt/exp_soft/gromacs-2016.1
GAAS 0.1.7 Bioinformatic tool to calculate accurate community composition and average genome size in metagenomes /opt/exp_soft/GAAS-0.17/
Gaussian 9 Computational chemistry LICENSE RESTRICTED
GATK 3.3 The Genome Analysis Toolkit /opt/exp_soft/GATK
GATK 3.4.6 The Genome Analysis Toolkit /opt/exp_soft/GATK-3.4.6
GMT 5 Generic Mapping Tools /opt/exp_soft/GMT-5/bin
HyPhy 2.11 MPI beta Hypothesis testing using Phylogenies /opt/exp_soft/hyphyMPI/bin
IDL 8.3 IDL is the trusted scientific programming language used across disciplines /opt/exp_soft/IDL
Interproscan 5.14.53 InterPro is a database which integrates together predictive information about proteins function from a number of partner resource /opt/exp_soft/interproscan
IGV 2.1.24 Visualization tool for interactive exploration of large integrated genomic datasets /opt/exp_soft/IGV
Java 1.7.0 Java Runtime Environment /opt/exp_soft/java/jdk1.7.0_75/
Java 1.8.0 Java Runtime Environment /opt/exp_soft/java/jdk1.8.0_31/
jModeltest2 2.1.4 Statistical selection of best-fit models of nucleotide substitution /opt/exp_soft/jModelTest-2.1.4/
Julia Lang 0.3.0.2 Julia is a high-level high-performance dynamic programming language for technical computing /opt/exp_soft/julia-0.3.0.2
Karma 1.7.5 Karma is a toolkit for interprocess communications /opt/exp_soft/karma-1.7.25
Krona 2.4 Hierarchical data browser /opt/exp_soft/KronaTools-2.4
LASTZ 1.0.2 Designed to handle sequences the size of human chromosomes /opt/exp_soft/lastz-1.02
ls-dyna R7.0.0 Strongly coupled multi-physics solver /opt/exp_soft/ls-dyna
ls-opt 5.1.1 Design Optimization and Probabilistic Analysis package with an interface to LS-DYNA /opt/exp_soft/lsopt-5.1.1
Mafft 7.221 MAFFT is a multiple sequence alignment program for unix-like operating systems $PATH
Mauve 2015 Whole genome multiple alignment computations /opt/exp_soft/mauve
Monolix 2016R1 Model based drug development computing package /opt/exp_soft/Lixoft
Montage 4.0 Astronomical Image Mosaic Engine /opt/exp_soft/galfacts/montage
Mothur 1.3.6 Bioinformatics software for the microbial ecology community module load software/mothur-1.36.1
mpi4py 1.3 MPI implentation for Python /opt/exp_soft/python-2.7.3/bin
mpiBLAST 1.6.0 Software for comparing primary biological sequence information /usr/bin/mpiblast
mpich 3.2 Message Passing Interface for parallel computing module load mpi/mpich-3.2
Mr Bayes 3.2.1 Bayesian estimation of phylogeny - MPI version /opt/exp_soft/MrBayes-3.2.1/
Muscle 3.8.31 Multiple sequence alignment /opt/exp_soft/muscle3.8.31
NAMD 2.9 Molecular dynamics simulation package /opt/exp_soft/NAMD_2.9/
NAMD 2.9 GPU Molecular dynamics simulation package /opt/exp_soft/NAMD-2.9-CUDA-IB-SMP/
nasp 1.5 Nucleic Acid Structures Predictor /opt/exp_soft/nasp-1.5/
ncbi-blast 2.2.28+ Software for comparing primary biological sequence information /opt/exp_soft/ncbi-blast
nco 4.4.8 netCDF data analyzer /opt/exp_soft/nco-4.4.8
nest 2.4.1 Simulator for spiking neural network models /opt/exp_soft/nest-2.4.1
NumPy 1.7.1 open-source package for scientific computing with Python local version of Python only!
Octave 4.0.0 High-level interpreted language for numerical computations /opt/exp_soft/octave-4.0.0
OpenFOAM 2.2.1 Open source CFD software /opt/exp_soft/OpenFOAM-2.2.1
OpenMPI 1.8.8 Message Passing Interface for parallel computing module load mpi/openmpi-1.8.8
OpenMPI 1.10.1 Message Passing Interface for parallel computing module load mpi/openmpi-1.10.1
Orca 3.0.2 An ab initio DFT and semiempirical SCF-MO package /opt/exp_soft/orca-3.0.2
Pear 0.9.0 Pair-end read merger /opt/exp_soft/pear-0.9.0
Pear 0.9.6 Pair-end read merger /opt/exp_soft/pear-0.9.6
PhyML 3.1 Maximum-Likelihood Phylogenies /opt/exp_soft/PhyML-3.1/
PicardTools 1.98 Java-based command-line utilities that manipulate SAM files /opt/exp_soft/picard-tools-1.98
Platypus 0.8.1 Genomic software /opt/exp_soft/Platypus-0.8.1
PrinSEQ 0.20.4 Easy and rapid quality control and data preprocessing /opt/exp_soft/prinseq-lite-0.20.4/
PyFasta 0.5.1 fast memory-efficient pythonic access to fasta sequence files /opt/exp_soft/python-2.7.2/bin
Python 2.6.8 Interpreted general-purpose high-level programming language local to host
Python 2.7.2 Interpreted general-purpose high-level programming language /opt/exp_soft/python-2.7.2/bin
Python 2.7.3 Interpreted general-purpose high-level programming language /opt/exp_soft/python-2.7.3/bin
QUANTUMESPRESSO 5.0.3 Chemistry package for electronic-structure calculations and materials modeling at the nanoscale /opt/exp_soft/espresso-5.0.3
R 3.1.0 Statistical computing and graphics $PATH
R 2.5.12 Statistical computing and graphics /opt/exp_soft/R-2.15.0/bin
R 3.0.0 Statistical computing and graphics /opt/exp_soft/R-3.0.0/bin
R 3.0.1 Statistical computing and graphics /opt/exp_soft/R-3.0.1/bin
R 3.0.2 Statistical computing and graphics /opt/exp_soft/R-3.0.2/bin
R 3.2.0 Statistical computing and graphics /opt/exp_soft/R-3.2.0/bin
R 3.3.0 Statistical computing and graphics /opt/exp_soft/R-3.3.0/bin
RAxML 7.7.0 Maximum Likelihood based inference of large phylogenetic trees /opt/exp_soft/RAxML-7.7.0
RAxML 8.1.18 Maximum Likelihood based inference of large phylogenetic trees /opt/exp_soft/RAxML-8.1.18
RepeatMasker 4.0.5 RepeatMasker screens DNA sequences for interspersed repeats and low complexity DNA sequences /opt/exp_soft/repeatmasker
Root CERN 6.0.5 An object oriented framework for large scale data analysis /opt/exp_soft/root-6.0.5
RTGtools 3.5.2 Utilities to easily manipulate and accurately compare multiple VCF files /opt/exp_soft/rtg-tools-3.5.2/
samblaster 0.1.22 A tool to mark duplicates and extract discordant and split reads from sam files /opt/exp_soft/samblaster-master
SAMtools 0.1.19 flexible generic format for storing nucleotide sequence alignment /opt/exp_soft/samtools-0.1.19
SAMtools 1.1 flexible generic format for storing nucleotide sequence alignment /opt/exp_soft/samtools-1.1
SAMtools 1.2 flexible generic format for storing nucleotide sequence alignment /opt/exp_soft/samtools-1.2
SciPy 0.13 open-source software for mathematics science and engineering local version of Python only!
SeqMonk 0.34.1 Mapped Sequence Analysis Tool /opt/exp_soft/SeqMonk-0.34.1
seqtk 1.0 Fast and lightweight tool for processing sequences in the FASTA or FASTQ format /opt/exp_soft/seqtk
SHAPEIT 2.5 fast and accurate method for estimation of haplotypes from genotype or sequencing data /opt/exp_soft/shapeit
smalt 0.7.5 SMALT efficiently aligns DNA sequencing reads with a reference genome /opt/exp_soft/smalt-0.7.5/
snpEff 3.5 Genetic variant annotation and effect prediction toolbox /opt/exp_soft/snpEff
snpEff 4.1H Genetic variant annotation and effect prediction toolbox /opt/exp_soft/snpEff-4.1H
SOAPdenovo 2 novel short-read assembly method /opt/exp_soft/SOAPdenovo/
SolexaQA 3.1.4 Calculates quality statistics and creates visual representations of data quality from second-generation sequencing technology /opt/exp_soft/Solexa-3.1.4
SPades 3.10.1 St. Petersburg genome assembler /opt/exp_soft/SPAdes-3.10.1-Linux/
Stata 13 Statistics - Graphics - Data Management /opt/exp_soft/Stata13
SGA 0.10.13 String Graph de novo Assembler /opt/exp_soft/sga/bin
T-COFFEE 10.00 Multiple sequence alignment package /opt/exp_soft/tcoffee
tabix 0.2.6 Generic indexer for TAB-delimited genome position file /opt/exp_soft/tabix-0.2.6
treemix 1.12 A method for inferring the patterns of population splits and mixtures /opt/exp_soft/treemix-1.12/
tophat 2.1.1 Fast splice junction mapper for RNA-Seq reads /opt/exp_soft/tophat-2.1.1
Trimmomatic 0.33 A flexible read trimming tool for Illumina NGS data /opt/exp_soft/Trimmomatic
UNAfold 3.8 Unified Nucleic Acid Folding and hybridization package $PATH
UV-CDAT 1 visual-data exploration and analysis capabilities for climate-data analysis /opt/exp_soft/uvcdat
VCFtools 0.1.12 Maps short reads to a reference genome /opt/exp_soft/vcftools_0.1.12
VCFtools 0.1.12 Maps short reads to a reference genome /opt/exp_soft/vcftools_0.1.12
VCFtools 0.1.13 Maps short reads to a reference genome /opt/exp_soft/vcftools_0.1.13
Velvet 1.2.10 Sequence assembler for very short reads /opt/exp_soft/velvet-1.2.10
VelvetOptimizer 2.2.5 VelvetOptimiser is a multi-threaded Perl script /opt/exp_soft/VelvetOptimiser-2.2.5
verifyBamID 1.1.1 verifies whether the reads in particular file match previously known genotypes for an individual /opt/exp_soft/verifyBamID-1.1.1
verifyBamID 1.1.2 verifies whether the reads in particular file match previously known genotypes for an individual /opt/exp_soft/verifyBamID-1.1.2
VMD 1.9.1 Visual Molecular Dynamics /opt/exp_soft/vmd-1.9.1/bin