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 |