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software_bioinformatics [2020/11/08 21:16]
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software_bioinformatics [2024/05/11 03:56] (current)
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-====== ​Aplicaciones Científicas ​======+====== ​Software y librerías disponibles ​======
  
 Bioinformatics,​ Chemistry, Physics, etc 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|W|X|Y|Z+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** |+| \\ **#** | \\ **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|+
 |**B** | | | | |**B** | | | |
-| |bowtie2 0.7.17|software ​package ​for mapping low-divergent ​sequences ​against a large reference genomesuch as the human genome+| |barrnap|0.9|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+| |bcftools|1.8|Set of utilities for variant calling and manipulation of variant call format ​(VCFfiles in genomics research.| 
-| |blast+|2.10.0(default)| | +| |bowtie2|2.5.3|A fast and memory-efficient alignment tool for mapping DNA sequencing reads to a reference genome
-| |blast|2.2.26| +| |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+
-| |bedops|2.4.38| | +
-| |beagle-lib|3.1.2| ​+
-| |bcftools|1.10.2| | +
-| |bbtools|38.86| | +
-| |barrnap|0.9| | +
-| | | | | +
-| | | | |+
 |**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|3.20.6|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-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|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): file format ​and set of software libraries used for storing and accessing multidimensional scientific data
-| \\  **1** | \\ Namd2| \\ 2019-11-27-multicore\\ Modelamiento Molecular| +|**O** | | | | 
-| \\  **2** | \\ gromacs| \\ 2019.4| \\ Modelamiento Molecular| +| |openfoam|v2312|Open-source computational fluid dynamics (CFD) software package ​for simulating complex fluid flows.| 
-| \\  **3** | \\ R| \\ 3.6.1| \\ Análisis estadístico| +| |openmpi|4.1.1|Open-source implementation ​of the Message Passing Interface (MPI) standard ​for parallel computingenabling efficient communication among distributed processes.
-| \\  **4** | \\ wrf| \\ 3.9.1| \\ Mesoscale numerical weather prediction+| |openmpi|4.1.6|Open-source implementation ​of the Message Passing Interface ​(MPIstandard ​for parallel computingenabling efficient communication among distributed processes.| 
-\\  **5** \\ wrf| \\ 4.0| \\ Mesoscale numerical weather prediction+|**P** | | | | 
-\\  **6** \\ netcdf/c| \\ 4.7.3| \\ Network Common Data Form| +| |parallel|20160722|A shell tool for executing jobs in parallelallowing ​for efficient and concurrent execution ​of tasks across multiple cores or machines.| 
-| \\  **7** | \\ netcdf/fortran| \\ 4.5.2| ​\\ Network Common Data Form+| |parsnp|2.0.5|Tool for rapid core-genome ​alignment ​and SNP detection
-| \\  **8** | \\ quantum-espresso/​schrodinger| \\ 6.4.1-2019-4| \\ Modelamiento Molecular| +| |pcre|2.10.43|PCRE (Perl Compatible Regular Expressions):​ A library ​for implementing regular expression pattern matching using syntax similar to Perl
-| \\  **11** | \\ cutadapt| \\ 2.10| \\ finds and removes adapter sequences, primers, poly-tails and other types of unwanted sequence from your high-throughput sequencing reads+| |perl|5.38.2|High-level, general-purpose programming language known for its versatility in text processing ​and system administration tasks.
-\\  ​**12** | \\ cufflinks\\ 2.2.1\\ Transcriptome assembly and differential expression analysis for RNA-Seq.+| |prank|170427|tool for the rapid and accurate generation ​of phylogenetic trees based on sequence alignment data
-\\  **13** ​\\ cpanm\\ 1.7044\\ perl utility| +| |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.| 
-| \\  **14** | \\ circos| \\ 0.69-9| \\ for visualizing data and informationIt visualizes data in a circular layout+| |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.| 
-\\  **15** ​\\ checkm\\ 1.1.2\\ set of tools for assessing the quality of genomes recovered from isolatessingle cells, or metagenomes+| |python|3.12.1|High-level programming languagewidely used for scriptingweb development,​ data analysis, and more.| 
-\\  **16** ​\\ cdhit\\ 4.8.1\\ Takes a fasta format sequence database as input and produces a set of '​non-redundant' ​(nr)…| +|**Q** | | | | 
-| \\  **17** | \\ canu| \\ 1.9| \\ Fork of the Celera Assembler designed ​for high-noise single-molecule sequencing| +| |qiime2|amplicon-2024.2-py38|A bioinformatics software package ​for analyzing ​and visualizing microbial community data generated from high-throughput sequencing ​technologies
-| \\  **18** | | | | +|**R** | | | | 
-| \\  **19** | | | | +| |R|4.4.0|A programming language and environment ​for statistical computing ​and graphics, widely used in data analysis, statistical modeling, and visualization
-| \\  **20** | | | \\ Alineamiento de secuencias de tipo localya sea de ADN, ARN o de proteínas.| +| |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.| 
-\\  ​**21** | | | \\ Alineamiento de secuencias de tipo local, ya sea de ADN, ARN o de proteínas+|**S** | | | | 
-\\  **22** ​| | | \\ Alineamiento de secuencias de tipo localya sea de ADN, ARN o de proteínas| +| |samtools|1.9|Suite of programs ​for interacting with high-throughput sequencing ​data
-| \\  **23** | | | \\ swiss-army knife of tools for a wide-range ​of genomics analysis ​tasks.| +| |singularity|4.1.0|Containerization platform designed ​for HPC environmentsfacilitating reproducibility and portability ​of software stacks.| 
-\\  **24** ​| | | \\ highly scalable and easily-parallelizable ​genome ​analysis toolkit¶| +|**T** | | | | 
-| \\  **25** | | | \\ high-performance library that can perform the core calculations at the heart of most Bayesian ​and Maximum Likelihood phylogenetics+| |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.| 
-\\  **26** ​| | | \\ set of utilities that manipulate variant calls| +| |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.| 
-| \\  **27** | | | \\ suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.| +|**U** | | | | 
-| \\  **28** | | | \\ predicts the location of ribosomal RNA genes in genomes| +|**V** | | | | 
-| \\  **29** | \\ ascp| \\ 3.9.9| | +|**W** | | | | 
-| \\  **30** | \\ bamtools| \\ 2.5.1\\ toolkit ​for handling BAM files.+|**X** | | | | 
-\\  **31** ​\\ diamond\\ 0.9.35\\ molecular ​and crystal structure visualization software+|**Y** | | | | 
-\\  **32** ​\\ eggnog-mapper\\ 2.0.1\\ tool for functional annotation ​of large sets of sequences ​based on fast orthology assignments using precomputed clusters+|**Z** | | | | 
-\\  **33** ​\\ EMBOSS\\ 6.6.0| \\ European Molecular Biology Open Software Suite| +| |zlib|1.2.13|A versatile compression library for data compression and decompression.|
-| \\  **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| \\ identifyingaligningmasking and visualizing archaeal 16Sbacterial 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| \\ 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 filterreformat ​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 fastmemory-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| \\ 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| +
-| \\  **92** | \\ hmmer| \\ 2.3.2\\ biosequence analysis using profile hidden Markov models .| +
-| \\  **93** | \\ hmmer| \\ 3.1b1| \\ biosequence analysis using profile hidden Markov models .| +
-| \\  **94** | \\ hmmer| \\ 3.1b2| \\ biosequence analysis using profile hidden Markov models .| +
-| \\  **95** | \\ hmmer| \\ 3.2.1| \\ biosequence analysis using profile hidden Markov models .| +
- +
-\\+
  
  
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