Software List

Generate AMR classifiers using a bespoke implementation that is designed for finding the k-mers that are indicative of resistance

CLUMPY is dedicated to the calculation of γ-ray or neutrino signals from annihilating and decaying astrophysical Dark Matter.

CMake cross-platform make system.

Compute the probability distribution of gene tree histories and gene tree topolgies for a fixed three-taxon species tree under the coalescent model with gene flow between both pairs of sister population.

Constraints-based modeling of biological networks.

COMSOL is multiphysics simulation software. Note, COMSOL is no longer supported and is available ‘as is’. We do not have an active support agreement with COMSOL, and we cannot obtain newer releases. COMSOL is only available from the Flux on-campus cluster.

A program for unsupervised binning of metagenomic contigs

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] CONVERGE is a CFD code with adaptive meshing.

CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.

CPLEX is a high-performance optimizer for linear programming

flappie: Basecall Fast5 reads using flip-flop basecalling

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats.

crystal evaluates crystaline solids.

CUBIT is a full-featured software toolkit for robust generation of two- and three-dimensional finite element meshes.

CUDA compilers and libraries.

cuDNN libraries.

Transcriptome assembly and differential expression analysis for RNA-Seq.

CUDA Profiler Tools Interface

cutadapt removes adapter sequences fromnhigh-throughput sequencing data. This is usually necessary when the readnlength of the sequencing machine is longer than the molecule that isnsequenced, for example when sequencing microRNAs.

CYANA is a program for automated structure calculation of biological macromolecules on the basis of conformational constraints from NMR.

The Cython compiler for writing C extensions for the Python language

Dalton is an integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale.

Dalton is an integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale.

Delly2 is an integrated structural variant prediction method

Dendropy is a Python library for phylogenetic computing.

DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.

This software is Open Source. Disco is a multi threaded and multiprocess distributed memory overlap-layout-consensus (OLC) metagenome assembler

DMTCP is a tool to transparently checkpoint the state of multiple simultaneous applications, including multi-threaded and distributed applications.

DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK.

DSK: disk streaming K-mers.

Dynare is a software platform for handling a wide class of economic models, in particular dynamic stochastic general equilibrium (DSGE) and overlapping generations (OLG) models.

software package for Bayesian inference of shared evolutionary events

EEMS uses the concept of effective migration to model the relationship between

egglib-cpp a C++ library for evolutionary genetics and genomics

The EIGENSOFT package implements methods from the following 2 papers:Patterson et al. 2006 PLoS Genet 2:e190 (population structure) Price et al. 2006 Nat Genet 38:904-9 (EIGENSTRAT stratification correction)

ELSA: Extended Local Similarity Analysis

EMBOSS is The European Molecular Biology Open Software Suite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.

EMIRGE reconstructs full length ribosomal genes from short read sequencing data.

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).

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] EnSight is a post processing and visualization tool.