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software_bioinformatics [2024/04/22 03:51] admin |
software_bioinformatics [2024/05/11 03:56] (current) admin |
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| | \\ **#** | \\ **Aplicación** | \\ **Versión** | \\ **Descripción** | | | \\ **#** | \\ **Aplicación** | \\ **Versión** | \\ **Descripción** | | ||
| |**A** | | | | | |**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** | | | | | |**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.| | | |bcftools|1.8|Set of utilities for variant calling and manipulation of variant call format (VCF) files in genomics research.| | ||
| + | | |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** | | | | | |**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|3.15.4|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.| | | |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** | | | | | |**D** | | | | | ||
| |**E** | | | | | |**E** | | | | | ||
| + | | |expat|2.6.2|Fast, lightweight, and robust XML parser library written in C.| | ||
| |**F** | | | | | |**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|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** | | | | | ||
| | |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.| | ||
| |**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| | ||
| + | | |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** | | | | | |**I** | | | | | ||
| + | | |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|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** | | | | | |**K** | | | | | ||
| |**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.| | ||
| + | | |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** | | | | | |**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** | | | | | |**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| | ||
| |**O** | | | | | |**O** | | | | | ||
| - | | |openfoam|5.0|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.| | ||
| |**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.| | ||
| + | | |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.| | ||
| + | | |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.| | | |python|3.12.1|High-level programming language, widely used for scripting, web development, data analysis, and more.| | ||
| |**Q** | | | | | |**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** | | | | | ||
| + | | |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** | | | | | |**S** | | | | | ||
| | |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| | ||
| Line 41: | Line 88: | ||
| |**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.| | ||
| |**U** | | | | | |**U** | | | | | ||
| |**V** | | | | | |**V** | | | | | ||
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| |**Y** | | | | | |**Y** | | | | | ||
| |**Z** | | | | | |**Z** | | | | | ||
| + | | |zlib|1.2.13|A versatile compression library for data compression and decompression.| | ||