Software List

A suite of CAE software products.

XCrySDen is a molecular/crystal structure visualization program.

A Practical Iterative De Bruijn Graph De Novo Assembler related to Sequence assembly problem in bioinfomatics.

IDL analysis and visualization software.

Image libraries

ImageMagick is a software suite to create, edit, compose, or convert bitmap images.

Intel MPI runtime library.

IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes. Most people use just a couple of the program’s basic functions, but we have also built up a collection of specialized and powerful options. If you are new to IMPUTE2, or indeed to phasing and imputation in general, we suggest that you start by learning the basics.

Indri is a search engine that provides state-of-the-art text search and a rich structured query language for text collections

Intel compiler suite.

Intel Threading Building Blocks (Intel TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable and composable, and that have future-proof scalability.

scan sequences against InterPro’s signatures

a swiss-army knife of tools for a wide-range of genomics analysis tasks.

Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale ?nonlinear optimization.

ipyrad is a toolbox for assembly and analysis of RAD-seq type genomic data sets

ITensor—Intelligent Tensor—is a C++ library for implementing tensor network calculations.

Software tools for image analysis..

JAGS is Just Another Gibbs Sampler. It is a program for analysis of

Oracle Java JRE

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.

Julia is a high-level, high-performance dynamic language for technical computing. The main homepage for Julia can be found at julialang.org.

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

Jim Kent command line bioinformatic utilities

KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files.

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] Knitro is an optimization software library for finding solutions of both continuous optimization models as well as discrete optimization models with integer or binary variables. Knitro is primarily designed for finding local optimal solutions of large sacle continuous nonlinear problems.

kSNP does SNP discovery and SNP annotation from whole genomes

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] Lahey Fortran – f95/f90 fortran compiler

LAMMPS is a classical molecular dynamics code that models an ensemble of particles.

LAPACK is written in Fortran 90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.

Determine and mark up significant differences between LATEX files

A simple utility for executing multiple sequential or multi-threaded applications in a single multi-node batch job

A gravitational lensing software for modeling mass distribution of galaxies and clusters (strong and weak regime).

Guile-based library implementing flexible control files for scientific simulations.

liftOver converts genome coordinates between assemblies

LIGGGHTS stands for LAMMPS improved for general granular and granular heat transfer simulations.

LocusZoom is designed to facilitate viewing of local association results together with useful information about a locus.

Large Scale Blast Score Ratio

LS-DYNA finite element analysis software.

LS-DYNA finite element analysis software.

Lua is a powerful, efficient, lightweight, embeddable scripting language. It supports procedural programming, object-oriented programming, functional programming, data-driven programming, and data description.