| Software Item | Details | ||||||
|---|---|---|---|---|---|---|---|
| genblast | genBlast is a computational gene prediction program that is based on protein homology
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| geneid | geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure.
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| genometools | The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt.
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| genscan | GENSCAN is a general-purpose gene identification program
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| geos | GEOS (Geometry Engine – Open Source) is a C++ port of the Java Topology Suite (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced topology functions.
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| gepard | Gepard allows the calculation of 5 dotplots even for large sequences like chromosomes or bacterial genomes.
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| gffcompare | The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the ‘query’ files), when compared with a reference annotation (also provided as GFF).
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| ghostscript | Ghostscript is an interpreter for the PostScript language and for PDF.
|
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| git | Git version control software
|
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| glimmer | Microbial Gene-Finding System
|
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| GlimmerHMM | Eukaryotic Gene-Finding System
|
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| globus | Provides an interface to Globus services from the shell, and is suited to both interactive
|
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| gloome | A C++ shell program for the detection of gain ans loss events
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| gmt | an open source collection of tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x–y plots via contour maps to artificially illuminated surfaces and 3D perspective views.
|
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| go | Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
|
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| gotcloud | GotCloud contains Mapping & Variant Calling Pipelines.
|
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| gpaw | GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE).
|
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| gromacs | GROMACS performs Newtonian simulatons of molecular dynamics.
|
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| gsl | GNU scientific libraries
|
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| gstreamer | GStreamer is a library for constructing graphs of media-handling components.
|
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| GTDBTk | GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. It is computationally efficient and designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes.
|
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| gtsuite | GT-SUITE is a versatile multi-physics platform for constructing models of general systems.
|
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| gubbins | Genealogies Unbiased By recomBinations In Nucleotide Sequences
|
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| gurobi | Gurobi optimization problem solver.
|
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| hadoop | Configure Java for Hadoop
|
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| harminv | Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion – given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.
|
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| hdf | HDF 4 data libraries and utilities.
|
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| hdf5 | HDF5 data libraries and utilities.
|
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| hdf5-par | HDF5 data libraries and utilities.
|
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| helios | [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] HELIOS Generalized Geometry Lattice Analysis package. Includes Casmo and Simulate from teh Studsvik suite.
|
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| hello | Hello world example of writing a module.
|
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| hic-pro | HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps.
|
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| hisat2 | HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome).
|
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| hmmer | HMMER: biosequence analysis using profile hidden Markov models
|
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| hmmer2 | a swiss-army knife of tools for a wide-range of genomics analysis tasks.
|
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| homer | HOMER is a suite of tools for Motif Discovery and ChIP-Seq analysis.
|
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| hspice | HSPICE is a electrial circuit simulation package
|
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| HTSeq | a swiss-army knife of tools for a wide-range of genomics analysis tasks.
|
||||||
| htslib | C library for high-throughput sequencing data formats
|
||||||
| hydra | Hydra launcher with Torque support.
|
Total pages: 13
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