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

#	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.
	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
	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
	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
	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
	infernal	1.1.5	A software suite for searching sequence databases using covariance models (CMs) and profile stochastic context-free grammars (SCFGs).
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
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
	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
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
	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
	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.
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
X
Y
Z
	zlib	1.2.13	A versatile compression library for data compression and decompression.