Bioinformatics, Chemistry, Physics, etc
índice : A|B|C|D|E|F|G|H|I|J|K|L|M|N|O|P|Q|R|S|T|U|V|W|X|Y|Z
| # | Aplicación | Versión | Descripción |
| A | |||
| aragorn | 1.2.36 | A software tool for predicting tRNA genes in DNA sequences, used for annotating genomes and identifying transfer RNA genes with high accuracy. | |
| B | |||
| barrnap | 0.9 | A software tool for predicting ribosomal RNA (rRNA) genes in DNA sequences, used for annotating genomes and identifying rRNA genes with high accuracy. | |
| 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. | |
| 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 | |
| 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 | |
| C | |||
| cd-hit | 4.6.8-2017-0621 | A fast and efficient clustering tool for sequence analysis, commonly used in bioinformatics to identify and remove redundancy within large sets of sequences. | |
| cmake | 3.15.4 | Cross-platform build system generator, widely used for managing the build process of software projects. | |
| cmake | 3.20.6 | Cross-platform build system generator, widely used for managing the build process of software projects. | |
| cpanm | 1.7047-perl-5.38.2 | Lightweight command-line tool for installing Perl modules from CPAN. | |
| curl | 8.7.1 | A command-line tool and library for transferring data with URLs, supporting a wide range of protocols including HTTP, HTTPS, FTP, and more. | |
| D | |||
| 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. | |
| F | |||
| fastqc | 0.12.1 | A quality control tool for high-throughput sequencing data, commonly used to assess the quality of raw sequence data generated by next-generation sequencing (NGS) platforms | |
| fasttree | 2.1.10 | A tool for inferring approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences | |
| fftw | 3.3.10 | 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 | |||
| 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 | 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 | |||
| 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 | |
| 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. | |
| I | |||
| infernal | 1.1.5 | A software suite for searching sequence databases using covariance models (CMs) and profile stochastic context-free grammars (SCFGs). | |
| 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. | |
| 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 | 17.0.10 | JDK (Java Development Kit): A set of software tools and libraries for developing Java applications, including compilers, debuggers, and class libraries | |
| K | |||
| 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. | |
| 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. | |
| libidn | 1.33 | A library for handling Internationalized Domain Names (IDN), providing support for encoding and decoding domain names containing non-ASCII characters. | |
| libncurses | 6.5 | A programming library that provides an API for creating text-based user interfaces (TUI) in a terminal environment | |
| libnsl | 1.2.0 | A library providing support for Network Services Library (NSL) functions, including name and address resolution, used for network communication in Unix-based systems. | |
| libnsl | 1.3.0 | A library providing support for Network Services Library (NSL) functions, including name and address resolution, used for network communication in Unix-based systems. | |
| libnsl | 2.0.1 | A library providing support for Network Services Library (NSL) functions, including name and address resolution, used for network communication in Unix-based systems. | |
| libpng | 1.6.43 | A platform-independent library that contains C functions for handling PNG images. | |
| libreadline | 8.2 | A library for creating interactive command-line interfaces (CLI) with advanced line-editing capabilities, including command history, completion, and customizable key bindings. | |
| libtirpc | 1.0.2 | A library providing transport-independent RPC (Remote Procedure Call) protocol support, facilitating communication between distributed applications over a network. | |
| libtirpc | 1.3.4 | A library providing transport-independent RPC (Remote Procedure Call) protocol support, facilitating communication between distributed applications over a network. | |
| M | |||
| mafft | 7.310 | A versatile and accurate multiple sequence alignment program, widely used for aligning nucleotide and protein sequences to infer evolutionary relationships. | |
| mcl | 14-137 | MCL (Markov Cluster Algorithm): A graph clustering algorithm used to identify clusters in large networks or graphs. | |
| minced | 0.4.2 | Is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in full genomes or environmental datasets such as assembled contigs from metagenomes. | |
| miniconda3 | 24.3.0 | Lightweight distribution of the Conda package manager and Python environment | |
| N | |||
| ncbi-blast | 2.6.0-libnsl-1.2.0-libidn-1.33 | 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 | |
| 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 | |||
| 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 | 4.1.6 | 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 | |||
| parallel | 20160722 | A shell tool for executing jobs in parallel, allowing for efficient and concurrent execution of tasks across multiple cores or machines. | |
| parsnp | 2.0.5 | Tool for rapid core-genome alignment and SNP detection | |
| 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. | |
| 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 | |
| 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. | |
| prokka | 1.14.6 | A software tool for annotating bacterial, archaeal, and viral genomes, used for predicting protein-coding genes, identifying non-coding RNAs, and annotating genomic features with functional information. | |
| python | 3.12.1 | High-level programming language, widely used for scripting, web development, data analysis, and more. | |
| Q | |||
| qiime2 | amplicon-2024.2-py38 | A bioinformatics software package for analyzing and visualizing microbial community data generated from high-throughput sequencing technologies | |
| R | |||
| R | 4.4.0 | A programming language and environment for statistical computing and graphics, widely used in data analysis, statistical modeling, and visualization | |
| roary | 3.12 | A tool for rapidly identifying core and accessory genes from bacterial genome assemblies, used in comparative genomics studies to analyze bacterial pan-genomes and assess genomic diversity. | |
| S | |||
| 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 | 4.2.1 | Containerization platform designed for HPC environments, facilitating reproducibility and portability of software stacks. | |
| 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. | |
| 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 | |||
| 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 | |||
| 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 | |||
| Y | |||
| Z | |||
| zlib | 1.2.13 | A versatile compression library for data compression and decompression. |