software_bioinformatics [WIKI CEMCC]

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====== Software y librerías disponibles ======

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

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| \\ **#** | \\ **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.|