Aplicaciones Científicas

 **#** | \\
 **Aplicación** | \\
 **Versión** | \\
 **Descripción** |

 **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|