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software_bioinformatics [2024/09/16 17:58] 127.0.0.1 external edit |
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| | |bedtools|2.27.1|A powerful suite of tools for genomic analysis, providing functionality for the manipulation, comparison, and annotation of genomic intervals stored in BED format| | | |bedtools|2.27.1|A powerful suite of tools for genomic analysis, providing functionality for the manipulation, comparison, and annotation of genomic intervals stored in BED format| | ||
| | |bcftools|1.8|Set of utilities for variant calling and manipulation of variant call format (VCF) files in genomics research.| | | |bcftools|1.8|Set of utilities for variant calling and manipulation of variant call format (VCF) files in genomics research.| | ||
| + | | |blas|3.12.0|A library that provides efficient, low-level routines for performing basic vector and matrix operations.| | ||
| | |bowtie2|2.5.3|A fast and memory-efficient alignment tool for mapping DNA sequencing reads to a reference genome| | | |bowtie2|2.5.3|A fast and memory-efficient alignment tool for mapping DNA sequencing reads to a reference genome| | ||
| | |bzip2|1.0.8|A compression utility and file format used to compress and decompress files, known for its high compression ratio and efficient compression algorithms| | | |bzip2|1.0.8|A compression utility and file format used to compress and decompress files, known for its high compression ratio and efficient compression algorithms| | ||
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| |**D** | | | | | |**D** | | | | | ||
| |**E** | | | | | |**E** | | | | | ||
| + | | |elmer|9.0|Elmer FEM is an open-source multiphysics simulation software designed for modeling complex physical phenomena in various scientific and engineering applications.| | ||
| | |expat|2.6.2|Fast, lightweight, and robust XML parser library written in C.| | | |expat|2.6.2|Fast, lightweight, and robust XML parser library written in C.| | ||
| |**F** | | | | | |**F** | | | | | ||
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| | |fftw|3.3.10-openmp-threads|FFTW (Fastest Fourier Transform in the West) is a highly efficient library for computing discrete Fourier transforms.| | | |fftw|3.3.10-openmp-threads|FFTW (Fastest Fourier Transform in the West) is a highly efficient library for computing discrete Fourier transforms.| | ||
| |**G** | | | | | |**G** | | | | | ||
| + | | |getdp|3.5.0|GetDP (General Environment for the Treatment of Discrete Problems) is a finite element solver that provides flexible tools for solving partial differential equations, widely used in electromagnetic, thermal, and mechanical simulations.| | ||
| | |gromacs|2019.4-fftw-3.3.10-openmpi-4.1.1|Molecular dynamics simulation software widely used for biomolecular studies.| | | |gromacs|2019.4-fftw-3.3.10-openmpi-4.1.1|Molecular dynamics simulation software widely used for biomolecular studies.| | ||
| | |gromacs|2024.1-fftw-3.3.10-openmpi-4.1.6|Molecular dynamics simulation software widely used for biomolecular studies.| | | |gromacs|2024.1-fftw-3.3.10-openmpi-4.1.6|Molecular dynamics simulation software widely used for biomolecular studies.| | ||
| + | | |gromacs|2024.1-fftw-3.3.10-openmpi-5.0.3|Molecular dynamics simulation software widely used for biomolecular studies.| | ||
| + | | |gsl|2.6|GSL (GNU Scientific Library) is a collection of numerical computing routines that offer a range of mathematical functions and algorithms, including linear algebra, statistics, and numerical integration.| | ||
| + | | |gsl|2.7.0|GSL (GNU Scientific Library) is a collection of numerical computing routines that offer a range of mathematical functions and algorithms, including linear algebra, statistics, and numerical integration.| | ||
| |**H** | | | | | |**H** | | | | | ||
| | |harvest|1.1.2|A suite of tools for analyzing and visualizing genomic data, it provides functionalities for genome alignment, synteny analysis, and visualization of genomic features| | | |harvest|1.1.2|A suite of tools for analyzing and visualizing genomic data, it provides functionalities for genome alignment, synteny analysis, and visualization of genomic features| | ||
| + | | |hdf5|1.14.4-2-with-java-fortran|HDF5 (Hierarchical Data Format version 5): A versatile and high-performance file format and library for managing and storing large and complex datasets| | ||
| | |hdf5|1.14.4-2|HDF5 (Hierarchical Data Format version 5): A versatile and high-performance file format and library for managing and storing large and complex datasets| | | |hdf5|1.14.4-2|HDF5 (Hierarchical Data Format version 5): A versatile and high-performance file format and library for managing and storing large and complex datasets| | ||
| | |hmmer|3.4|A software suite for searching sequence databases using profile hidden Markov models (HMMs), used for protein sequence analysis, homology detection, and functional annotation.| | | |hmmer|3.4|A software suite for searching sequence databases using profile hidden Markov models (HMMs), used for protein sequence analysis, homology detection, and functional annotation.| | ||
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| | |infernal|1.1.5|A software suite for searching sequence databases using covariance models (CMs) and profile stochastic context-free grammars (SCFGs).| | | |infernal|1.1.5|A software suite for searching sequence databases using covariance models (CMs) and profile stochastic context-free grammars (SCFGs).| | ||
| |**J** | | | | | |**J** | | | | | ||
| + | | |jasper|2.0.33|JPEG-2000 reference software, commonly used for encoding and decoding images in the JPEG-2000 format, with support for various image compression and decompression functionalities.| | ||
| | |jasper|4.2.4|JPEG-2000 reference software, commonly used for encoding and decoding images in the JPEG-2000 format, with support for various image compression and decompression functionalities.| | | |jasper|4.2.4|JPEG-2000 reference software, commonly used for encoding and decoding images in the JPEG-2000 format, with support for various image compression and decompression functionalities.| | ||
| | |jdk|8.0_41|JDK (Java Development Kit): A set of software tools and libraries for developing Java applications, including compilers, debuggers, and class libraries| | | |jdk|8.0_41|JDK (Java Development Kit): A set of software tools and libraries for developing Java applications, including compilers, debuggers, and class libraries| | ||
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| |**L** | | | | | |**L** | | | | | ||
| | |lammps|17Apr2024-openmpi-4.1.6|Large-scale Atomic/Molecular Massively Parallel Simulator, a versatile molecular dynamics software package for simulating a wide range of materials and biological systems.| | | |lammps|17Apr2024-openmpi-4.1.6|Large-scale Atomic/Molecular Massively Parallel Simulator, a versatile molecular dynamics software package for simulating a wide range of materials and biological systems.| | ||
| + | | |lapack|3.12.0|Builds upon BLAS and offers a comprehensive suite of routines for solving more complex linear algebra problems, including systems of linear equations, eigenvalue problems, and singular value decompositions.| | ||
| | |libdb|5.3.28|A library providing high-performance embedded database functionality, commonly used in applications requiring efficient data storage and retrieval.| | | |libdb|5.3.28|A library providing high-performance embedded database functionality, commonly used in applications requiring efficient data storage and retrieval.| | ||
| | |libidn|1.33|A library for handling Internationalized Domain Names (IDN), providing support for encoding and decoding domain names containing non-ASCII characters.| | | |libidn|1.33|A library for handling Internationalized Domain Names (IDN), providing support for encoding and decoding domain names containing non-ASCII characters.| | ||
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| | |ncbi-blast |2.13.0|BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.| | | |ncbi-blast |2.13.0|BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.| | ||
| | |netcdf |c-4.7.3-fortran-4.5.2|NetCDF (Network Common Data Form): A file format and set of software libraries used for storing and accessing multidimensional scientific data| | | |netcdf |c-4.7.3-fortran-4.5.2|NetCDF (Network Common Data Form): A file format and set of software libraries used for storing and accessing multidimensional scientific data| | ||
| + | | |nextflow |24.04.4|Nextflow is a workflow management software that facilitates the development and execution of scalable, reproducible computational pipelines, particularly for data-intensive tasks in bioinformatics.| | ||
| |**O** | | | | | |**O** | | | | | ||
| | |openfoam|v2312|Open-source computational fluid dynamics (CFD) software package for simulating complex fluid flows.| | | |openfoam|v2312|Open-source computational fluid dynamics (CFD) software package for simulating complex fluid flows.| | ||
| | |openmpi|4.1.1|Open-source implementation of the Message Passing Interface (MPI) standard for parallel computing, enabling efficient communication among distributed processes.| | | |openmpi|4.1.1|Open-source implementation of the Message Passing Interface (MPI) standard for parallel computing, enabling efficient communication among distributed processes.| | ||
| | |openmpi|4.1.6|Open-source implementation of the Message Passing Interface (MPI) standard for parallel computing, enabling efficient communication among distributed processes.| | | |openmpi|4.1.6|Open-source implementation of the Message Passing Interface (MPI) standard for parallel computing, enabling efficient communication among distributed processes.| | ||
| + | | |openmpi|5.0.3|Open-source implementation of the Message Passing Interface (MPI) standard for parallel computing, enabling efficient communication among distributed processes.| | ||
| + | | |openmpi|5.0.3-with-ucx|Open-source implementation of the Message Passing Interface (MPI) standard for parallel computing, enabling efficient communication among distributed processes.| | ||
| |**P** | | | | | |**P** | | | | | ||
| | |parallel|20160722|A shell tool for executing jobs in parallel, allowing for efficient and concurrent execution of tasks across multiple cores or machines.| | | |parallel|20160722|A shell tool for executing jobs in parallel, allowing for efficient and concurrent execution of tasks across multiple cores or machines.| | ||
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| | |pcre|2.10.43|PCRE (Perl Compatible Regular Expressions): A library for implementing regular expression pattern matching using syntax similar to Perl| | | |pcre|2.10.43|PCRE (Perl Compatible Regular Expressions): A library for implementing regular expression pattern matching using syntax similar to Perl| | ||
| | |perl|5.38.2|High-level, general-purpose programming language known for its versatility in text processing and system administration tasks.| | | |perl|5.38.2|High-level, general-purpose programming language known for its versatility in text processing and system administration tasks.| | ||
| + | | |pmix|4.1.3|PMIx (Process Management Interface for Exascale) is a scalable communication interface designed to optimize resource management and data exchange among processes in high-performance computing environments.| | ||
| + | | |pmix|4.2.7|PMIx (Process Management Interface for Exascale) is a scalable communication interface designed to optimize resource management and data exchange among processes in high-performance computing environments.| | ||
| + | | |pmix|5.0.2-openmpi-4.1.1|PMIx (Process Management Interface for Exascale) is a scalable communication interface designed to optimize resource management and data exchange among processes in high-performance computing environments.| | ||
| + | | |pmix|5.0.2|PMIx (Process Management Interface for Exascale) is a scalable communication interface designed to optimize resource management and data exchange among processes in high-performance computing environments.| | ||
| | |prank|170427|A tool for the rapid and accurate generation of phylogenetic trees based on sequence alignment data| | | |prank|170427|A tool for the rapid and accurate generation of phylogenetic trees based on sequence alignment data| | ||
| | |prodigal|2.6.3|A software tool for predicting protein-coding genes in DNA sequences, used for annotating genomes and identifying protein-coding genes with high accuracy.| | | |prodigal|2.6.3|A software tool for predicting protein-coding genes in DNA sequences, used for annotating genomes and identifying protein-coding genes with high accuracy.| | ||
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| | |samtools|1.9|Suite of programs for interacting with high-throughput sequencing data| | | |samtools|1.9|Suite of programs for interacting with high-throughput sequencing data| | ||
| | |singularity|4.1.0|Containerization platform designed for HPC environments, facilitating reproducibility and portability of software stacks.| | | |singularity|4.1.0|Containerization platform designed for HPC environments, facilitating reproducibility and portability of software stacks.| | ||
| + | | |singularity|4.2.1|Containerization platform designed for HPC environments, facilitating reproducibility and portability of software stacks.| | ||
| |**T** | | | | | |**T** | | | | | ||
| | |tabix|0.2.5|Tool for indexing and querying large tab-delimited text files, commonly used in genomics research for efficient retrieval of specific genomic regions.| | | |tabix|0.2.5|Tool for indexing and querying large tab-delimited text files, commonly used in genomics research for efficient retrieval of specific genomic regions.| | ||
| | |table2asn|1.28.943|A command-line tool for converting structured data tables into GenBank submission files, used for annotating DNA sequences and preparing submissions to the GenBank database.| | | |table2asn|1.28.943|A command-line tool for converting structured data tables into GenBank submission files, used for annotating DNA sequences and preparing submissions to the GenBank database.| | ||
| |**U** | | | | | |**U** | | | | | ||
| + | | |ucx|1.17.0|UCX (Unified Communication X) is a high-performance communication library that provides a unified framework for efficient and scalable data transfers across multiple network architectures, including InfiniBand, Ethernet, and shared memory.| | ||
| |**V** | | | | | |**V** | | | | | ||
| |**W** | | | | | |**W** | | | | | ||
| + | | |wrf|4.5.2-wps-4.5|WRF (Weather Research and Forecasting Model) is a powerful numerical weather prediction system designed for both atmospheric research and operational forecasting, widely used for simulating real-time weather phenomena on a regional scale.| | ||
| |**X** | | | | | |**X** | | | | | ||
| |**Y** | | | | | |**Y** | | | | | ||