Applications

Applications installed on ALICE and SPECTRE. This list is not exhaustive and does not include common Linux utilities.

Application versions

Both ALICE and SPECTRE use CentOS 7.6 .

Generally there is a module available for each item in the list. Use the module command to see which versions of an application are available, for example for Fluent:

> module avail fluent
--------------------- /cm/shared/modulefiles ------------------
fluent/16.2 fluent/18

Some applications have been built multiple times to suit the compilers available on the system. For example NetCDF has been built for the GCC and Intel. A module exists for each one so you can choose the most appropriate.

Install an application

If you need to install an application on ALICE and SPECTRE, contact the IT Service Desk.

List of applications

You can find more information about the applications by following the links in the tables below.  The links on the application names go to documentation at the University of Leicester. Links on the supplier names go to the supplier’s website.

A

Software
Version
Module
Licence
Supplier
Description
ABySS 2.0.1
1.9.0
abyss/2.0.1
abyss/1.9.0
Free Canada's Michael Smith Genome Science Centre De novo paired-end short sequence assembler
abinit
8.0.8
abinit/8.0.8
Free/OSS
The ABINIT Group Molecular dynamics simulation
AdapterRemoval 2.2.2 adapterremoval/2.2.2 Free/OSS AdapterRemoval team Removal of remnant adapter sequences from HTS data.
Affymetric Power Tools 1.16.1 affymetrix/1.16.1 Free/OSS Affymetrix, Inc. Tools for Affymetrix GeneChip arrays
ALLPATHS-LG 48894 allpathslg/48894 Free/OSS Broad Institute Whole genome shotgun assembler
Amber
16
14
amber/16
amber/14
Site licence
Ambermd.org
Amber molecular dynamics package
ANNOVAR 2017-07-17
2016-02-02
annovar/20170717
annovar/20160201
Free/OSS ANNOVAR team Annotation of genetic variants
APT 26.0.4
25.2.2
25.0.4

apt/26.0.4
apt/25.2.2
apt/25.0.4

Free/OS
Space Telescope Science Institute
Astronomer's proposal tool for HST and JWST
AstroConda 20171018
20170130
20161130
astroconda/20171018
astroconda/20170130
astroconda/20161130
Free/OSS STScI Python environment for STScI

B

Software
Version
Module
Licence
Supplier
Description
BBMap 36.47 bbmap/36.47 Free/OSS Lawrence Berkeley National Laboratory Short read aligner and other tools
BCFtools 1.9
1.8
bcftools/1.9
bcftools/1.8
Free/OSS SAMTools team Reading/writing BCF2/VCF/gVCF files
BEAT
6.10.1
beat/6.10.1
Free/OSS
S & T
Basic Envisat Atmospheric Toolbox
bedtools
2.25.0
bedtools/2.25.0
Fress/OSS
Aaron Quinlan Flexible suite of utilities for comparing genomic features
blas 3.6.0
blas/gcc/3.6.0
blas/intel/3.6.0
Free/OSS Netlib
Basic Linear Algebra Sub-programs
BLASR 5.3 blasr/5.3 Free/OSS University of California Basic Local Alignment with Successive Refinement tool
BLAST+
2.5.0
blast+/2.5.0
Free NCBI C++ Implementation of BLAST
Boost 1.64.0
1.62.0
boost/gcc/1.64.0
boost/gcc/1.62.0
Free/OSS Boost Community C++ libraries
BreakDancer 1.4.5 breakdancer/1.4.5 Free/OSS McDonnell Genome Institute Genome-wide detection of structural variants from next generation paired-end sequencing reads.
Bridger 2014-12-01 bridger/20141201 Free/OSS Bridger authors de-novo transcriptome assembler
BWA
0.7.17
0.7.16a
0.7.15
0.7.12
bwa/0.7.17
bwa/0.7.16a
bwa/0.7.15
bwa/0.7.12
Free/OSS
BWA Team
Burrows-Wheeler Aligner

C

Software
Version
Module
Licence
Supplier
Description
CASA 4.7.1
casa/4.7.1
Free/OSS National Radio Astronomy Observatory Common Astronomy Software Applications
CD-HIT 4.6.6 cd-hit/4.6.6 Free/OSS Sanford-Burnham Medical Research Institute Comparison of protein or nucleotide sequences
CFITSIO 3.410 cfitsio/3.410 Free/OSS NASA GSFC C routines for FITS files
CGA Tools 1.8.0.1 cgatools/1.8.0.1 Free/OSS Complete Genomics Complete Genomics analysis tools
ChromoPainterv2 20171211 chromopainter/20171211 Free/OSS GLOBETROTTER team Chromosome painting
CIAO 4.9
ciao/ciao-4.9
Free/OSS Chandra team Chandra X-ray Data Analysis Software (includes CALDB)
Circos 0.65-5 circos/0.65-5 Free/OSS Martin Krzywinski Circular visualisation
Clustal 20161012 clustal/20161012 Free/OSS University College Dublin Tools for multiple alignment of nucleic acid and protein sequences: clustalw, clustalx, clustalo
CMake 3.10.2
3.7.2
3.6.2
cmake/3.10.2
cmake/3.7.2
cmake/3.6.2
Free/OSS Kitware Make system
CNS
1.3
cns/1.3
Free/OSS
CNS team
Crystallography and NMR system
CNVnator 0.3.3 cnvnator/0.3.3 Free/OSS Abyzov Lab, Mayo Clinic CNV discovery tool
COMSOL Multiphysics 5.4 comsol/5.4 Teaching only COMSOL Physics simulations
COPEread 1.2.5 coperead/1.2.5 Free/OSS COPEread team

Connecting Overlapped Pair-End reads tools

ctools 1.4.3 ctools/1.4.3 Free/OSS L'Institut de Recherche en Astrophysique et Planétologie Cherenkov Telescope Array science analysis
Cufflinks 2.2.1
cufflinks/2.2.1 Free/OSS Cufflinks team Transcript assembly, differential expression, and differential regulation for RNA-Seq
cutadapt 1.11 cutadapt/1.11 Free/OSS Marcel Martin High-throughput sequence data cutter

D

Software
Version
Module
Licence
Supplier
Description
DaViT 0.7 davit/0.7 Free/OSS DaViT team SuperDARN visualisation toolkit
DeNovoGear 0.5.4 denovogear/0.5.4 Free/OSS DeNovoGear team Detect denovo mutations using sequencing data of related individuals
DISCOVAR de novo 52488 discovar/52488 Free/OSS Broad Institute De novo genome assembler
doxygen1
1.8.5

Free/OSS Dimitri van Heesch Source code documentation system
DS9

7.5
7.4
7.3.2

ds9/7.5
ds9/7.4
ds9/7.3.2

Free/OSS Smithsonian Astrophysical Observatory Astronomical imaging and data visualization

E

Software
Version
Module
Licence
Supplier
Description
Eigen 3.3.3 eigen/3.3.3 MPL2 free license OSS C++ linear algebra template library.
EMBOSS
6.6.0
emboss/6.6.0
Free/OSS
EMBOSS
Molecular Biology software suite. Includes Jemboss 1.5
EVidenceModeler 1.1.1 evidencemodeler/1.1.1 Free/OSS EVidence Modeler team Gene prediction tool
exonerate
2.4.0
2.2.0a
exonerate/2.4.0
exonerate/2.2.0a
Free/OSS
Guy Slater
Pairwise sequence comparison / alignment tool

F

Software
Version
Module              
Licence
Supplier
Description
FASTA
3.6
fasta/36
Free/OSS
University of Virginia
Protein / DNA search tool
FastQC 0.11.5 fastqc/0.11.5 Free/OSS Babraham Institute Quality control tool for high-throughput sequence data
FASTX-Toolkit
0.0.14
0.0.13
fastx-toolkit/0.0.14
fastx_toolkit/0.0.13
Free/OSS Assaf Gordon + contributors
Short-Reads FASTA/FASTQ preprocessing
FCM 2017-02 fcm/2017.02 Free/OSS Met Office
Source code build / management tools 
Fermi Tools
10r0p5
fermi/10r0p5
Free/OSS Goddard Space Flight Centre Fermi gamma ray telescope analysis tools
FERRET
7.0
ferret/7.0
Free/OSS
NOAA/OAR/PMEL Data visualisation
FFTW3 3.3.6 fftw/3.3.6 Free/OSS FFTW Discrete fourier/cosine/sine transform library
Filtlong 0.2.0 filtlong/0.2.0 Free/OSS Filtlong team Filter long reads by quality
FinchTV
1.3.1
finchtv/1.3.1
Free
Geospiza, Inc.
DNA sequence trace viewer
Firefox
52.5

Free/OSS
Mozilla Foundation
Web browser
FL (Fawlty Language)
0.79
fl/0.79
Free/OSS
Lajos Földy IDL clone
FLASH 1.2.11 flash/1.2.11 Free/OSS Johns Hopkins University Centre for Computational Biology Fast Length Adjustment of SHort reads tool
Fluent
16.2
fluent/16.2 25 users
ANSYS
CFD
FreeBayes 1.1.0 freebayes/1.1.0 Free/OSS Erik Garrison, Gabor Marth Bayesian haplotype-based polymorphism discovery and genotyping

G

Software
Version
Module
Licence
Supplier
Description
GATK 3.8
3.6
gatk/3.8
gatk/3.6
Free - restricted Broad Institute Genome Analysis Toolkit
GAUSS
17
15
gauss/17
gauss/15
6 Users
Aptech
Mathematical and statistical data analysis environment
GAUSS Runtime
17
15

gauss/grtm/17
gauss/grtm/15

Commercial Aptech
GAUSS Runtime for compiled GAUSS code
Gaussian g16
g03e01
gaussian/g16
gaussian/g03e01
Restricted Gaussian, Inc. Electronic structure modelling
GCC
6.3
6.1
5.4
4.8.5
gcc/6.3
gcc/6.1
gcc/5.4
Free/OSS
GNU
C/C++/Fortran compilers
GDAL
2.1.3
2.1.2
gdal/2.1.3
gdal/2.1.2
Free/OSS
Frank Warmerdam / GDAL developers
Translator library for raster geospatial data formats
GDL 0.9.7
0.9.6
gdl/0.9.7
gdl/0.9.6
Free/OSS GNU IDL clone
Ghostview
3.7.4

Free/OSS
Ghostscript team
PostScript viewer
Ghostscript
9.07

Free/OSS
Ghostscript Team
PostScript interpreter
gifsicle
1.87

Free/OSS
Eddie Kohler
Animated GIF creator
git
2.11.0
git/2.11.0
Free/OSS
Git
Version control software
Glimmer
3.02
glimmer/3.02
Free/OSS University of Maryland
Genetics
GLOBETROTTER 20171208 globetrotter/20171208 Free/OSS GLOBETROTTER team Chromosome painting
GMAP/GSNAP 2017-11-15 gmap/20171115 Free/OSS GMAP team Genomic mapping and alignment tools
gnuplot
5.2.2
5.0.0
4.2.6

gnuplot/5.2.2
gnuplot/5.0.0
gnuplot/5.0.0

Free/OSS
Gnuplot team
Data visualisation
Grace
5.1.25
grace/5.1.25
Free/OSS
Grace team
Data visualisation
GROMACS
2016.4
5.1.4
gromacs/2016.04
gromacs/5.1.4
Free/OSS

Molecular dynamics
GSL
1.15

Free/OSS
GNU
Scientific library for C/C++.

H

Software
Version
Module                    
Licence
Supplier
Description
HapCompass 0.8.2 hapcompass/0.8.2 Free/OSS Istrail Lab, Brown University Creation of haplotype assemblies
HDF5

1.8.17

hdf5/gcc/1.8.17
hdf5/gcc_mpi/1.8.17
hdf5/intel/1.8.17
hdf5/intel_mpi/1.8.17

Free/OSS HDF Group Data model library
HDF4
4.2.12
hdf4/gcc/4.2.12
hdf4/intel/4.2.12
Free/OSS HDF Group
HEASoft 6.22.1
6.21
6.20
6.19
heasoft/6.22.1
heasoft/6.21
heasoft/6.20
heasoft/6.19
Free/OSS NASA / HEASARC X-Ray Astronomy / FITS file tools
HipSTR 0.5 hipstr/0.5 Free/OSS Thomas Willems Genotyping of short tandem repeats
HTSlib 1.9
1.8
htslib/1.9
htslib/1.8
Free/OSS SAMTools team High-throughput sequencing library

I

Software
Version
Module                              
Licence
Supplier
Description
IDL

8.5
8.4
8.2
8.0
7.0

idl/idl85
idl/idl84
idl/idl82
idl/idl80
idl/idl70
Restricted ITT VIS Data analysis programming language
IDL Astronomy User's Library

2016-10-17

idlastro/20161017

Free / BSD 2
NASA Goddard Space Flight Center
Low-level IDL astronomy software 
IGV 2.3.82 igv/2.3.82 Free/OSS Broad Institute Interactive Genomics Viewer
ImageMagick1 6.7.8.9
Free/OSS ImageMagick team Bitmap image tools
Impute2
2.3.2
impute2/2.3.2
Free
University of Oxford
Genotype imputation and phasing
Intel Compilers
18
17
16
intel/compilers/18
intel/compilers/17
intel/compilers/16
5 users
Intel
Intel C/C++/Fortran compilers
Intel MPI
18
17.1
intel/mpi/18
intel/impi/17.1
ALICE
Intel
Intel MPI parallel programming libraries

J

Software
Version
Module
Licence
Supplier
Description
Java JDK 1.8
1.7
java/1.8
java/1.7
Free Oracle Programming language
Jemboss
1.5
emboss/6.6.0


See EMBOSS
joe
3.7

Free/OSS
Joseph Allen
Text editor

K

Software

Version
Module                        
Licence
Supplier
Description
kallisto 0.43.0 kallisto/0.43.0 Free/OSS University of California RNA-Seq transcript analysis
KAT
2.3.4
kat/12.3.4
Free/OSS
TGAC
k-mer spectra analysis
khmer 2.0
khmer/2.0 Free/OSS khmer team k-mer sequence analysis

L

Software
Version
Module                        
Licence
Supplier
Description
LAPACK
3.6.1
lapack/gcc/3.6.1
lapack/intel/3.6.1
Free/OSS
Netlib
Linear algebra routines for F90
log4cxx 0.10.0 log4cxx/0.10.1 Free/OSS Apache Software Foundation C++ logging framework

M

Software
Version
Module
Licence
Supplier
Description
MANTIS 1.0.4 mantis/1.0.4 Free/OSS Ohio State University College of Medicine Microsatellite Analysis for Normal-Tumor InStability
Mauve 2.4.0
2.3.9
mauve/2.4.0
mauve/2.3.9
Free/OSS Genome Evolution Laboratory
Multiple genome alignment
MATLAB

2018a
2016b
2016a
2015a
2013a

matlab/2018a
matlab/2016b
matlab/2016a
matlab/2015a
matlab/2013a

Commercial
MathWorks
High level programming language
MGEScan-non-LTR 2 mgescan/2 Free/OSS Indiana University Identification of non-LTR retrotransposons in genomic sequences
MIRA 4.0.2 mira/4.0.2 Free/OSS mira team Whole genome shotgun and EST sequence assembler
Modeller 9.19 modeller/9.19 Free/OSS University of California San Francisco

Modelling of protein structures

MOLDEN 5.7 molden/5.7 Free/OSS Nijmegen Centre for Molecular and Biomolecular Informatics Molecular density pre- and post-processor
molly 1.1.8 molly/1.1.8 Free/OSS Tom Marsh 1D astronomical spectra analysis
Mothur
1.38.1
mothur/1.38.1
Free/OSS
Patrick Schloss
Microbial ecology bioinformatics tool
mrsFAST-Ultra 3.4.0 mrsfast/3.4.0 Free/OSS mrsFAST-Ultra team Micro read substitution-only Fast Alignment Search Tool
MultiQC 1.3 multiqc/1.3 Free/OSS MultiQC team Bioinformatics reporting tool
MUMmer 3.23 mummer/3.23 Free/OSS MUMmer team Ultra-fast alignment of large-scale DNA and protein sequences
MuSiC2 0.2 music2/0.2 Free/OSS MuSiC2 team Cancer mutation analysis

N

Software
Version
Module                        
Licence
Supplier
Description
NAG
Various
nag/product
Commercial
NAG
Numerical libraries for C, Fortran
NAMD 2.12 namd/cpu/2.12
namd/gpu/2.12
Free/OSS University of Illinois Molecular dynamics simulation
Nano 3.0
2.9.8
2.9.2
nano/3.0
nano/2.9.8
nano/2.9.2
Free/OSS Nano team Text editor
Nanofilt 2.0.0 nanofilt/2.2.0 Free/OSS Wouter De Coster Filtering and trimming of Oxford Nanopore data
NanoPlot 1.0.0 nanoplot/1.0.0 Free/OSS Wouter De Coster Plotting of Oxford Nanopore data
NASA Baselibs
2.2.0
nasa-baselibs/2.2.0
Free/OSS
NASA
A collection of libraries used by the GEOS5 software
NetCDF
4.4.1
netcdf/gcc/4.4.1
netcdf/gcc-mpi/4.4.1
netcdf/intel/4.4.1
netcdf/intel-mpi/4.4.1
Free/OSS
Unidata
Data model library
Netpbm1
10.61.02
Free/OSS
Netpbm team
Bitmap image tools

O

Software
Version
Module                       
Licence
Supplier
Description
OpenFOAM 4.0
3.2
2.2.2
openfoam-extend/4.0-gcc
openfoam-extend/3.2-gcc
openfoam/2.2.2
Free/OSS OpenFOAM Foundation Computational fluid dynamics
OpenMPI
2.0.2
2.0.1
2.0.0
openmpi/gcc/2.0.2
openmpi/gcc/2.0.1
openmpi/gcc/2.0.0
openmpi/intel/2.0.1
openmpi/intel/2.0.0
Free/OSS
OpenMPI team
MPI parallel programming interface

P

Software
Version
Module                         
Licence
Supplier
Description
Panseq 3.2.1 panseq/3.2.1 Free/OSS Panseq team Pan-genomic sequence analysis
Period04 1.2.0 period4/1.2.0 Free/OSS TOPS Group, Universität Wien Analysis of large astronomical time series
Perl
5.24.0
5.16.3
perl/5.24.0
Free/OSS
Perl community
Perl programming language interpreter
PhaseTank 1.0 phasetank/1.0 Free/OSS PhaseTank team RNA characterisation
picard 2.6.0
2.1.0
picard/2.6.0
picard/2.1.0
Free/OSS The Broad Institute Java tools for next generation sequencing data
Pindel 0.2.5b8 pindel/0.2.5b8 Free/OSS Washington University School of Medicine Detection of structural variants in NGS data
Platanus 1.2.4 platanus/1.2.4 Free/OSS Tokyo Institute of Technology de novo genome assembler
plink
1.90
1.0.7
plink/1.90
plink/1.0.7
Free/OSS
Shaun Purcell
Whole genome association analysis tool
PLINK/SEQ 0.10 plinkseq/0.10 Free/OSS Massachusetts General Hospital Human genetic variation tools
PolSARpro 5.0.4 polsarpro/5.0.4 Free/OSS ESA Polarimetric SAR data processing tool
Porechop 0.2.3 porechop/0.2.3 Free/OSS Porechop team Adapter trimmer for Oxford Nanopore reads
poretools 0.6.0 poretools/0.6.0 Free/OSS poretools team Oxford Nanopore sequencing data tools
PRINSEQ 0.20.4 prinseq/0.20.4 Free/OSS Robert Schmeider Trimming and formatting of genomic data
PROJ.4 4.9.3 proj/4.9.3 Free/OSS Open Source Geospatial Foundation Cartographic projections library
Prokka 1.11 prokka/1.11 Free/OSS Victorian Bioinformatics Consortium
Prokaryotic genomes rapid annotation
pymol 1.8.4.0 pymol/1.8.4.0 Free/OSS Schrödinger
A molecular visualization system on an open source foundation
Python
3.5
2.7

python/gcc/35
python/gcc/27
python/intel/35
python/intel/27

Free/OSS
Python Software Foundation Programming language

Q

Software
Version
Module
Licence
Supplier
Description
QCTOOL
1.4
qctool/1.4
Free
QCTOOL Team
Control of GWAS data sets
QDOAS
3.2
2.111
qdoas/3.2
qdoas/2.111
Free/OSS
BIRA-IASB and S[&]T atmospheric chemistry, differential optical absorption spectroscopy
QIIME
2018.6
2018.4
2017.10
1.9.1
qiime2/2018.6
qiime2/2018.4
qiime2/2017.10
qiime/1.9.1
Free/OSS
qiime
pipeline for performing microbial community analysis
Qt 5.8.0
4.8.6
qt/5.8.0
qt/4.8.6
Free/OSS Digia UI framework
Qualimap 2.2.1 qualimap/2.2.1 Free/OSS Qualimap team
Quality control of alignment sequence data
QUAST 4.3
quast/4.3 Free/OSS Russian Academy of Sciences Quality Assessment Tool for genome assemblies

R

Software
Version
Module
Licence
Supplier
Description
R (including RStudio) 3.5.1
3.4.1
3.3.1
R/3.5.1
R/3.4.1
R/3.3.1
Free/OSS R team Statistical computing
RAREMETALWORKER 4.14.0 raremetalworker/4.14.0 Free/OSS Centre for Statistical Genetics Rare variants and gene level meta analysis
REAPR 1.0.18 reapr/1.0.18 Free/OSS Sanger Institute Tool for Recognising Errors in Assemblies using Paired Reads
RELION 2.1b1-gpu
2.1b1
2.0
relion/2.1b1-gpu
relion/2.1b1
2.0
Free/OSS MRC Laboratory of Molecular Biology Cry-EM analysis tool
ROOT
6.10.02
ROOT/6.10.02
Free/OSS
CERN
Object oriented programming environment
Rosetta
2017.45.59812
2015.39.58186
rosetta/2017.45.59812
rosetta/2015.39.58186
Free/OSS
Rosetta Commons
Macromolecular modelling
RSEM 1.3.0 rsem/1.3.0 Free/OSS Biostatistics & Medical Informatics, Univerisity of Wisconsin RNA sequencing by expectation-maximisation
RSeQC 2.6.4 rseqc/2.6.4 Free/OSS RSeQC team RNA-seq Quality Control Package
Ruby
2.0.0

Free/OSS
Ruby community
Programming language

S

Software
Version
Module
Licence
Supplier
Description
SAMtools
1.9
1.8
1.3.2
1.3.1
samtools/1.9
samtools/1.8
samtools/1.3.2
samtools/1.3.1
Free/OSS
SAMtools team
SAM-format sequence alignment tools
SAS 9.3 sas/9.3 Restricted SAS Institute Statistical analysis
SHAPEIT
2.837
shapeit/2.837
Free
Olivier Delanneau Haplotype inference tool
Snakemake 4.3.1 snakemake/4.3.1 Free/OSS Snakemake team Workflow creation tool
SnpEff 4.3t snpeff/4.3t Free/OSS Pablo Cingolani Genomic variant annotations and functional effect prediction toolbox
SNPtest
2.5.2 snptest/2.5.2
Free
University of Oxford
SNP analysis
SOAPdenovo 240 soapdenovo/240 Free/OSS Beijing Genomics Institute Short Oligonucleotide Analysis Package
SOAPdenovo-Trans 1.03 soapdenovo-trans/1.03 Free/OSS Beijing Genomics Institute de novo transcriptome assembler
SPAdes 3.9.0 spades/3.9.0 Free/OSS
St. Petersburg Academic University
St. Petersburg genome assembler for standard isolates and single-cell MDA bacteria assemblies
SRA Toolkit 2.8.0 sratoolkit/2.8.0 Free/OSS NCBI SRA tools
Staden
2.0.0
staden/2.0.0
Free/OSS
Sourceforge
DNA sequence assembly (Gap4 and Gap5), editing and analysis tools
STAR 2.5.2b star/2.5.2b Free/OSS Alex Dobbin Spliced Transcripts Alignment to a Reference
Starlink 2017A
2016A

starlink/2017A
starlink/2016A

Free/OSS Starlink team Astronomical data processing
STATA MP8
12
11
stata/12/mp8
stata/11/mp8
Restricted
STATA
Statistics, graphs and data management
STILTS 3.1
3.0.7
stilts/3.1
stilts/3.0.7
Free/OSS Astrophysics Group, Bristol University Starlink Tables Infrastructure Library Tool Set
Subversion1
1.9
subversion/1.9
Free/OSS
Apache Software Foundation
Version control client
SYBYL 7.3 sybyl/7.3 Restricted Tripos Computational chemistry and molecular modelling

T

Software
Version
Module
Licence
Supplier
Description
Tabix/bgzip
0.2.6
tabix/0.2.6
Free/OSS
SAM tools team
Generic indexer for TAB-delimited genome position files
Tablet 1.16.09.06 tablet/1.16.09.06 Free/OSS James Hutton Institute NGS assembly visualisation
Tecplot 360 2017R2
15.2
tecplot/2017R2
tecplot/15.2
Restricted Tecplot, Inc CFD post-processing
TOPCAT

4.5
4.4
4.3-3

topcat/4.5
topcat/4.4
topcat/4.3-3
Free/OSS Astrophysics Group, Bristol University Tool for OPerations on Catalogues And Tables
TopHat 3.3.6
tophat/3.3.6 Free/OSS TopHat team Fast splice junction mapper for RNA-Seq reads
Trans-ABySS 1.5.5 transabyss/1.5.5 Free/OSS Canada's Michael Smith Genome Sciences Centre Transcriptome data analysis pipeline
Transrate 1.0.3 transrate/1.0.3 Free/OSS Transrate team Transcriptome assembler
Trimmomatic 0.36
0.32
trimmomatic/0.36
trimmomatic/0.32
Free/OSS Trimmomatic team Illumina NGS read trimmer
Trinity 2.2.0 trinity/2.2.0 Free/OSS Trinity team RNA-seq assembler
Trinotate 3.0.1 trinotate/3.0.1 Free/OSS Trinotate team Transcriptome functional annotation and analysis
TrioCNV 0.1.2 triocnv/0.1.2 Free/OSS TrioCNV team CNV detection
Triodenovo 0.05 triodenovo/0.05 Free/OSS University of Michigan Centre for Statistical Genetics Bayesian framework for calling de novo mutations in trios for NGS data

U

Software
Version
Module
Licence
Supplier
Description
UDUNITS 2.2.26 udunits/2.2.26 Free/OSS UNIDATA Library for handling units of physical quantities

V

Software
Version
Module
Licence
Supplier
Description
Valgrind
3.12.0

Free/OSS
Valgrind team
Software analysis tool
VarScan

2.4.3
2.3.9

varscan/2.4.3
varscan/2.3.9
Free/OSS Washington University School of Medicine Variant calling and somatic mutation/CNV detection
VARTOOLS 1.34 vartools/1.34 Free/OSS Princeton University Tool for analysing light curves
VCFtools 0.1.14 vcftools/0.1.14 Free/OSS VCFtools team Tools for using Variant Call Format files
Velvet
1.2.10
velvet/1.2.10
Free/OSS
Daniel Zerbino / Ewan Birney
Sequence assembler for very short reads
VTK 8.0.1 VTK/8.0.1 Free/OSS Kitware, Inc. Visualisation toolkit

W

Software
Version
Module
Licence
Supplier
Description

X

Software
Version
Module
Licence
Supplier
Description
Xfig1
3.2.7a
3.2.5c
xfig/3.2.7a
Free/OSS
Xfig team
Illustration tool
XMM SAS
16.0.0
15.0.0
xmmsas/16.0.0
xmmsas/15.0.0
Free
ESA
XMM-Newton Science Analysis System

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