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| - | ====== Aplicaciones Científicas ====== | + | ====== Software y librerías disponibles ====== |
| Bioinformatics, Chemistry, Physics, etc | Bioinformatics, Chemistry, Physics, etc | ||
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| | \\ **#** | \\ **Aplicación** | \\ **Versión** | \\ **Descripción** | | | \\ **#** | \\ **Aplicación** | \\ **Versión** | \\ **Descripción** | | ||
| |**A** | | | | | |**A** | | | | | ||
| - | | |aragorn|1.2.38|tRNA (and tmRNA) detection| | + | | |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.| |
| - | | |arb|6.0.6|Phylogenetic analysis of rRNA and other biological sequences such as amino acids| | + | |
| - | | |ascp|3.9.9|–| | + | |
| |**B** | | | | | |**B** | | | | | ||
| - | | |bowtie2|0.7.17|software package for mapping low-divergent sequences against a large reference genome, such as the human genome| | + | | |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.| |
| - | | |bwa|2.4.1|alineación de secuencias y el análisis de secuencias en bioinformática| | + | | |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| |
| - | | |blast+|2.9.0|Alineamiento de secuencias de tipo local, ya sea de ADN, ARN o de proteínas| | + | | |bcftools|1.8|Set of utilities for variant calling and manipulation of variant call format (VCF) files in genomics research.| |
| - | | |blast+|2.10.0(default)|Alineamiento de secuencias de tipo local, ya sea de ADN, ARN o de proteínas| | + | | |bowtie2|2.5.3|A fast and memory-efficient alignment tool for mapping DNA sequencing reads to a reference genome| |
| - | | |blast|2.2.26|Alineamiento de secuencias de tipo local, ya sea de ADN, ARN o de proteínas| | + | | |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| |
| - | | |bedtools|2.29.2|swiss-army knife of tools for a wide-range of genomics analysis tasks| | + | |
| - | | |bedops|2.4.38|highly scalable and easily-parallelizable genome analysis toolkit| | + | |
| - | | |beagle-lib|3.1.2|high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics| | + | |
| - | | |bcftools|1.10.2|set of utilities that manipulate variant calls| | + | |
| - | | |bbtools|38.86|suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data| | + | |
| - | | |barrnap|0.9|predicts the location of ribosomal RNA genes in genomes| | + | |
| - | | |bamtools|2.5.1|toolkit for handling BAM files.| | + | |
| - | | | | | | | + | |
| |**C** | | | | | |**C** | | | | | ||
| - | | |cufflinks|2.10|finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads| | + | | |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.| |
| - | | |circos|2.2.1|Transcriptome assembly and differential expression analysis for RNA-Seq.| | + | | |cmake|3.15.4|Cross-platform build system generator, widely used for managing the build process of software projects.| |
| - | | |cutadapt|0.69-9|for visualizing data and information. It visualizes data in a circular layout| | + | | |cmake|3.20.6|Cross-platform build system generator, widely used for managing the build process of software projects.| |
| - | | |checkm|1.1.2|set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes| | + | | |cpanm|1.7047-perl-5.38.2|Lightweight command-line tool for installing Perl modules from CPAN.| |
| - | | |cdhit|4.8.1|Takes a fasta format sequence database as input and produces a set of 'non-redundant' (nr)…| | + | | |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.| |
| - | | |canu|1.9|Fork of the Celera Assembler designed for high-noise single-molecule sequencing| | + | |
| - | | | | | | | + | |
| - | | | | | | | + | |
| |**D** | | | | | |**D** | | | | | ||
| - | | |diamond|0.9.35|molecular and crystal structure visualization software| | ||
| |**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-openmp-threads|FFTW (Fastest Fourier Transform in the West) is a highly efficient library for computing discrete Fourier transforms.| | ||
| |**G** | | | | | |**G** | | | | | ||
| - | | |gromacs|2019.4|Modelamiento Molecular| | + | | |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.| | ||
| |**H** | | | | | |**H** | | | | | ||
| - | | |hmmer|2.3.2|biosequence analysis using profile hidden Markov models .| | + | | |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| |
| - | | |hmmer|3.1b1|biosequence analysis using profile hidden Markov models .| | + | | |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|3.1b2|biosequence analysis using profile hidden Markov models .| | + | | |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|3.2.1|biosequence analysis using profile hidden Markov models .| | + | |
| - | | | | | | | + | |
| |**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** | | | | | ||
| - | | |Namd2|2019-11-27-multicore|Modelamiento Molecular| | + | | |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** | | | | | ||
| + | | |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.| | ||
| |**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.| | ||
| |**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|3.6.1|Analísis Estadistico| | + | | |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.| | ||
| + | |**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** | | | | | ||
| + | |**V** | | | | | ||
| |**W** | | | | | |**W** | | | | | ||
| - | | |WRF|3.9.1|Mesoscale numerical weather prediction| | ||
| - | | |WRF|4.0|Mesoscale numerical weather prediction| | ||
| |**X** | | | | | |**X** | | | | | ||
| - | | \\ **6** | \\ netcdf/c| \\ 4.7.3| \\ Network Common Data Form| | + | |**Y** | | | | |
| - | | \\ **7** | \\ netcdf/fortran| \\ 4.5.2| \\ Network Common Data Form| | + | |**Z** | | | | |
| - | | \\ **8** | \\ quantum-espresso/schrodinger| \\ 6.4.1-2019-4| \\ Modelamiento Molecular| | + | | |zlib|1.2.13|A versatile compression library for data compression and decompression.| |
| - | | \\ **32** | \\ eggnog-mapper| \\ 2.0.1| \\ tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters| | + | |
| - | | \\ **33** | \\ EMBOSS| \\ 6.6.0| \\ European Molecular Biology Open Software Suite| | + | |
| - | | \\ **34** | \\ FastANI| \\ 1.3| \\ Produces accurate ANI estimates and is faster than alignment (e.g., BLAST)- based approaches.| | + | |
| - | | \\ **35** | \\ vcftools| \\ 0.1.17| \\ package designed for working with VCF files| | + | |
| - | | \\ **36** | \\ Unicycler| \\ 0.4.9b| \\ assembly pipeline for bacterial genomes| | + | |
| - | | \\ **37** | \\ tRNAscan-SE| \\ 2.0.5| \\ searches for tRNA genes in genomic sequences| | + | |
| - | | \\ **38** | \\ trinityrnaseq| \\ 2.11.0| \\ Trinity RNA-Seq de novo transcriptome assembly| | + | |
| - | | \\ **39** | \\ trf| \\ 4.09| \\ Analyze DNA sequences| | + | |
| - | | \\ **40** | \\ TransDecoder| \\ 5.5.0| \\ Assist in the identification of potential coding regions within ….| | + | |
| - | | \\ **41** | \\ tophat| \\ 2.1.1| \\ Alineación del rendimiento de las lecturas de secuenciación de cDNA …| | + | |
| - | | \\ **42** | \\ tbl2asn| \\ 3.10.0| \\ Automates the creation of sequence records for submission to GenBank| | + | |
| - | | \\ **43** | \\ ssu-align| \\ 0.1.1| \\ identifying, aligning, masking and visualizing archaeal 16S, bacterial 16S and eukaryotic 18S…| | + | |
| - | | \\ **44** | \\ sratoolkit| \\ 2.10.7| \\ Using the SRA Toolkit to convert .sra files into other formats …| | + | |
| - | | \\ **45** | \\ SPAdes| \\ 3.14.1| \\ Assembly toolkit containing various assembly pipelines.| | + | |
| - | | \\ **46** | \\ SPAdes| \\ 3.13.2| \\ Assembly toolkit containing various assembly pipelines.| | + | |
| - | | \\ **47** | \\ SINA| \\ 1.6.1| \\ accurate high-throughput multiple sequence alignment of ribosomal RNA genes.| | + | |
| - | | \\ **48** | \\ seqtk| \\ 1.3| \\ A fast and lightweight tool for processing sequences in the FASTA or FASTQ format.| | + | |
| - | | \\ **49** | \\ seqkit| \\ 0.12.1| \\ Seqkit is a tool for manipulating fasta and fastq files.| | + | |
| - | | \\ **50** | \\ samtools| \\ 1.10.2| \\ suite of programs for interacting with high-throughput sequencing data| | + | |
| - | | \\ **51** | \\ salmon| \\ 1.2.1| \\ Is a tool for quantifying the expression of transcripts using RNA-seq data.| | + | |
| - | | \\ **52** | \\ RSEM| \\ 1.3.3| \\ Tool for the quantification of RNA-seq data.| | + | |
| - | | \\ **53** | \\ roary| \\ 1.7.7| \\ Application for rapidly constructing pan genomes from large numbers of prokaryote sample| | + | |
| - | | \\ **54** | \\ racon| \\ 1.4.16| \\ Consensus sequence| | + | |
| - | | \\ **55** | \\ quast| \\ 5.1.0rc1| \\ Quality Assessment Tool for Genome Assemblies| | + | |
| - | | \\ **56** | \\ pyani| \\ 0.2.10| \\ a Python3 module that provides support for calculating average nucleotide identity (ANI)| | + | |
| - | | \\ **57** | \\ prokka| \\ 1.14.6| \\ tool for the rapid annotation of prokaryotic genomes| | + | |
| - | | \\ **58** | \\ prodigal| \\ 2.6.3| \\ Prodigal is an unsupervised machine learning algorithm| | + | |
| - | | \\ **59** | \\ prinseq| \\ 0.20.4| \\ Tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim …| | + | |
| - | | \\ **60** | \\ prank| \\ 170427| \\ Is a probabilistic multiple alignment program for DNA,| | + | |
| - | | \\ **61** | \\ pplacer| \\ 1.1.alpha17| \\ Places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference …| | + | |
| - | | \\ **62** | \\ htslib| \\ 1.10.2| \\ An implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, …| | + | |
| - | | \\ **63** | \\ mash| \\ 2.2| \\ Reduces large sequences and sequence sets to small, …| | + | |
| - | | \\ **64** | \\ mafft| \\ 7.470| \\ is a multiple sequence alignment program for unix-like operating systems| | + | |
| - | | \\ **65** | \\ ksnp| \\ 3.1.2| \\ Finds single nucleotide polymorphisms (SNPs) in whole genome data.| | + | |
| - | | \\ **66** | \\ krona| \\ 2.7.1| \\ powerful metagenomic visualization tool| | + | |
| - | | \\ **67** | \\ kaiju| \\ 1.7.3| \\ program for the taxonomic classification of high-throughput sequencing reads.| | + | |
| - | | \\ **68** | \\ jellyfish| \\ 2.3.0| \\ tool for fast, memory-efficient counting of k-mers in DNA.| | + | |
| - | | \\ **69** | \\ jdk| \\ 8.0_41| \\ Java Develop ToolKit| | + | |
| - | | \\ **70** | \\ jdk| \\ 14.0.1| \\ Java Develop ToolKit| | + | |
| - | | \\ **71** | \\ jdk| \\ 11.28| \\ Java Develop ToolKit| | + | |
| - | | \\ **72** | \\ infernal| \\ 1.1.3| \\ for searching DNA sequence databases for RNA structure and sequence similarities| | + | |
| - | | \\ **73** | \\ pilon| \\ 1.23| \\ an automated genome assembly improvement and variant detection tool| | + | |
| - | | \\ **74** | \\ picard| \\ 2.23.1| \\ a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.| | + | |
| - | | \\ **75** | \\ phyml| \\ 3.3.20190909| \\ is a phylogeny software based on the maximum-likelihood principle| | + | |
| - | | \\ **76** | \\ phylip| \\ 3.697| \\ a free package of programs for inferring phylogenies| | + | |
| - | | \\ **77** | \\ parallel| \\ 20200622| \\ Parallel is an indispensible tool for speeding up bioinformatics. It allows you to easily parallelize commands| | + | |
| - | | \\ **78** | \\ paml| \\ 4.9| \\ a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.| | + | |
| - | | \\ **79** | \\ ncftp| \\ 3.2.6| \\ cliente ftp| | + | |
| - | | \\ **80** | \\ muscle| \\ 3.8.31| \\ A program to create multiple sequence alignments of a large number of sequences| | + | |
| - | | \\ **81** | \\ MUMmer| \\ 3.23| \\ an open source software package for the rapid alignment of very large DNA and amino acid sequences| | + | |
| - | | \\ **82** | \\ mothur| \\ 1.44.1| \\ a single resource to analyze molecular data that is used by microbial ecologists| | + | |
| - | | \\ **83** | \\ minimap2| \\ 2.17| \\ pairwise alignment for nucleotide sequences.| | + | |
| - | | \\ **84** | \\ miniconda| \\ 4.8.3| \\ python minimalist| | + | |
| - | | \\ **85** | \\ MCL| \\ 14-137| \\ a cluster algorithm for graphs| | + | |
| - | | \\ **86** | \\ MinCED| \\ 0.4.2| \\ program to find Clustered Regularly Interspaced Short .| | + | |
| - | | \\ **87** | \\ fastqc| \\ 0.11.9| \\ a quality control application for high throughput sequence data.| | + | |
| - | | \\ **88** | \\ fasttree| \\ 2.1.11| \\ FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences| | + | |
| - | | \\ **89** | \\ Gblocks| \\ 0.91b| \\ computer program written in ANSI C language that eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein| | + | |
| - | | \\ **90** | \\ go| \\ 1.14.4| \\ compilador de lenguaje GO| | + | |
| - | | \\ **91** | \\ gtdbtk| \\ 1.2.0| \\ a toolkit to classify genomes with the Genome Taxonomy Database, B| | + | |