Medical Contributed Software
The following list of software is available on the Flux cluster Contributed from the Medical School. To access any of these packages, use the module load modulename command; for more information on the module command see our module documentation page.
Many of these packages have multiple versions, to see available versions, type module avail.
| Module Name | Versions | Description | Additional Information | ||
| BioPerl | 1.6.1 | BioPerl is Perl tools for Bioinformatics, genomics and Life Sciences. | Vendor Website |
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| VarScan | 2.2.11 | VarScan is a platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples | Vendor Website |
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| abyss | 1.2.3 | Abyss is a de novo sequence assembler that is designed for very short reads. The single-processor version is useful for assembling genomes up to 40-50 Mbases in size. The parellel version is implemented MPI and is capable of assembling larger genomes. | Vendor Website |
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| amber | 12.0 | Amber a set of molecular mechanical force fields for the simulation of biomolecules | CAC Documentation Vendor Website |
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| amber-bjg | 11.0-cuda-mpi 11.0-mpi |
ERROR:105: Unable to locate a modulefile for 'amber-bjg' | |||
| annovar | 1.0.0 | Annovar is is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes. | Vendor Website |
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| arb | 5.5 | The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. | Vendor Website |
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| autodock_vina | 1.1.2 | AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use. | Vendor Website |
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| bedtools | 2.10.1 2.16.2 |
BEDTools is a suite of utilties for comparing genomic features in BED format. These utilities allow one to quickly address such tasks as: 1. Intersecting two BED files. 2. Merge overlapping features. 3. Paired-end overlaps. | Vendor Website |
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| biopython | 1.60 | Biopython is a set of freely available tools for biological computation. | Vendor Website |
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| boost | 1.45.0 | Boost provides free peer-reviewed portable C++ source libraries. | Vendor Website Manual |
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| bowtie | 0.12.7 0.12.8 2.0.0-beta6 |
Ultrafast, memory-efficient short read aligner. Aligns short DNA sequences (reads) to the human genome. Uses a Burrows-Wheeler-Transformed BWT index. | Vendor Website |
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| breakdancer | 1.0 1.1 1.3 |
WashU structural variant (SV) detection algorithm for paired-end data. | Vendor Website |
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| bwa | 0.5.9 0.6.1 0.6.2 |
A BWT Alignment program - a progression from Maq. BWA is a fast light-weighted tool that aligns short sequences to a sequence database. By default BWA finds an alignment within distance 2 to the query sequence. | Vendor Website |
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| chimerascan | 0.4.5 | chimerascan is a software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets. | Vendor Website |
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| cufflinks | 0.9.1 1.3.0 2.0.0 2.0.1 |
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. | Vendor Website |
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| cython | 0.16 | Cython is a language that makes writing C extensions for the Python language as easy as Python itself. | Vendor Website |
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| desmond | 3.0.3.1 | Desmond is a software to carry out high speed molecular dynamic simulations of biological systems. | Vendor Website |
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| dindel | 1.01 | Dindel is a program for calling small indels from short-read sequence data ('next generation sequence data'). It is currently designed to handle only Illumina data. | Vendor Website |
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| eigensoft | 4.2 | The EIGENSOFT package combines functionality from the population genetics methods (Patterson et al. 2006) and EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker's variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. | Vendor Website |
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| epd | 6.2-2 | A python distribution for scientists that provides a comprehensive set of tools to perform data analysis and visualization. Academic version of license is installed. | Vendor Website |
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| exonerate | 2.2.0 | TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie. | Vendor Website |
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| fastqc | 0.10.0 0.10.1 |
FastQC is an application which takes a FastQ file and runs a series of tests on it to generate a comprehensive QC report. | Vendor Website |
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| gatk | 1.6 2.3-9 |
The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and local realigner. | Vendor Website |
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| gcc | 4.5.1 | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada | Vendor Website Manual |
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| gtool | 0.7.5 | GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. GTOOL can be used to: generate subsets of genotype data, to convert genotype data between the PED file format and the file format used by SNPTEST and IMPUTE, merge genotype datasets together, orient genotype data according to a strand file. | Vendor Website |
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| impute2 | 2.2.2 | IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes. | Vendor Website |
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| liftOver | 1.0.0 | liftOver is one of the UCSCBiotools. It moves annotations from one assembly to another. | Vendor Website |
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| maq | 0.7.1 | maq is software for builing genetic assemblies | Vendor Website |
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| meme | 4.9.0 | MEME is a tool for discovering motifs in a group of related DNA or protein sequences. | Vendor Website |
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| metal | 2011-03-25 | The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner. | Vendor Website |
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| mosaik | 1.1.0021 | MOSAIK is a reference-guided assembler for genetic sequences . | Vendor Website |
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| mothur | 1.27 1.29 |
Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. It incorporates the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more. | Vendor Website |
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| namd | 2.9 | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | Vendor Website Manual |
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| ncbi-blast | 2.2.26 | A BWT Alignment program - a progression from Maq. BWA is a fast light-weighted tool that aligns short sequences to a sequence database. By default BWA finds an alignment within distance 2 to the query sequence. | Vendor Website |
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| numexpr | 2.0.1 | The numexpr package supplies routines for the fast evaluation of array expressions elementwise by using a vector-based virtual machine. | Vendor Website |
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| openmpi | 1.4.3 | loads the OpenMPI/GCC compiler environment | Vendor Website Manual |
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| perl-modules | 1.0.0 | perl-modules is a collection of Perl modules. | Vendor Website |
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| picard | 1.32 1.53 1.70 1.71 1.79 |
Picard comprises Java-based command-line utilities that manupulate SAM files, and a Java API (SAM-JDK) for creating new programs that read SAM files. | Vendor Website |
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| plink | 1.07 | PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. | Vendor Website |
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| prism | 1_1_6 | PRISM is a software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. | Vendor Website |
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| pysam | 0.5 | Pysam is a python module for reading and manipulating Samfiles. | Vendor Website |
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| pytables | 2.4.0 | PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. | Vendor Website |
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| python3 | 3.2.3 | Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. | Vendor Website |
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| r-modules | 2.12.1 | The following R modules are included in this package: DNAcopy, doMC, foreach, IRanges, iterators, multicore, and readDepth. | Vendor Website |
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| repeatmasker | 3.3.0 | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). | Vendor Website |
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| rmblast | 1.2 | RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler. | Vendor Website |
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| samtools | 0.1.12a 0.1.18 |
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. | Vendor Website |
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| stampy | 1.0.16 | Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. | Vendor Website |
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| star | 2.1.1d | STAR aligns RNA-seq reads to a reference genome. | Vendor Website |
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| swig | 2.0.7 | SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. SWIG is used with a variety of target languages including common scripting languages such as Perl, PHP, Phython, Tcl and Ruby. SWIG is most commonly used to create high-level interpreted or compiled programming environments, user interfaces, and as a tool for testing and prototyping C/C++ software. | Vendor Website |
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| tmap | 1.1 | TMAP is a set of programs for building genetic maps, similar to CarthaGne, JoinMap, and MapMaker. | Vendor Website |
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| tophat | 1.1.0 1.4.0 2.0.0 2.0.3 2.0.4 2.0.5 |
TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie. | Vendor Website |
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| uchime | 4.2.40 | UCHIME is an algorithm for detecting chimeric sequences. | Vendor Website |
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| vat | 2.0.1 | VAT is a computational framework to functionally annotate variants in personal genomes using a cloud-computing environment. | Vendor Website |
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| velvet | 1.0.13 1.2.07 |
Velvet is a de novo genomic assembler specially designed for short read sequencing technologies such as Solexa or 454. | Vendor Website |
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