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Aplicaciones Científicas
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 | 1.2.38 | tRNA (and tmRNA) detection | |
| arb | 6.0.6 | Phylogenetic analysis of rRNA and other biological sequences such as amino acids | |
| ascp | 3.9.9 | – | |
| B | |||
| bowtie2 | 0.7.17 | software package for mapping low-divergent sequences against a large reference genome, such as the human genome | |
| bwa | 2.4.1 | alineación de secuencias y el análisis de secuencias en bioinformática | |
| blast+ | 2.9.0 | Alineamiento de secuencias de tipo local, ya sea de ADN, ARN o de proteínas | |
| blast+ | 2.10.0(default) | Alineamiento de secuencias de tipo local, ya sea de ADN, ARN o de proteínas | |
| blast | 2.2.26 | Alineamiento de secuencias de tipo local, ya sea de ADN, ARN o de proteínas | |
| 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 | |||
| cufflinks | 2.10 | finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads | |
| circos | 2.2.1 | Transcriptome assembly and differential expression analysis for RNA-Seq. | |
| cutadapt | 0.69-9 | for visualizing data and information. It visualizes data in a circular layout | |
| checkm | 1.1.2 | set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes | |
| cdhit | 4.8.1 | Takes a fasta format sequence database as input and produces a set of 'non-redundant' (nr)… | |
| canu | 1.9 | Fork of the Celera Assembler designed for high-noise single-molecule sequencing | |
| D | |||
| diamond | 0.9.35 | molecular and crystal structure visualization software | |
| E | |||
| F | |||
| G | |||
| gromacs | 2019.4 | Modelamiento Molecular | |
| H | |||
| hmmer | 2.3.2 | biosequence analysis using profile hidden Markov models . | |
| hmmer | 3.1b1 | biosequence analysis using profile hidden Markov models . | |
| hmmer | 3.1b2 | biosequence analysis using profile hidden Markov models . | |
| hmmer | 3.2.1 | biosequence analysis using profile hidden Markov models . | |
| I | |||
| J | |||
| K | |||
| L | |||
| M | |||
| N | |||
| Namd2 | 2019-11-27-multicore | Modelamiento Molecular | |
| P | |||
| Q | |||
| R | |||
| R | 3.6.1 | Analísis Estadistico | |
| W | |||
| WRF | 3.9.1 | Mesoscale numerical weather prediction | |
| WRF | 4.0 | Mesoscale numerical weather prediction | |
| X | |||
| 6 | netcdf/c | 4.7.3 | Network Common Data Form |
| 7 | netcdf/fortran | 4.5.2 | Network Common Data Form |
| 8 | quantum-espresso/schrodinger | 6.4.1-2019-4 | Modelamiento Molecular |
| 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 |