UTILIDADES DE ANÁLISIS

» BÚSQUEDA DE SECUENCIAS

» ANÁLISIS DEL ADN

     MANPULACIONES DEL ADN
     COMPOSICIÓN
     TRADUCCIÓN
     RESTRICCIÓN
     DISEÑO OLIGOS
    CÁLCULO TM
    BLAST/FASTA Y OTROS     
     ALINEAMIENTO DE 2 SECUENCIAS
     ALINEAMIENTO MÚLTIPLE
     CLUSTERING
     VECTORES
     DETECCIÓN DE GENES
     DETECCIÓN DE MOTIVOS DE ADN
     METILACIÓN
     OTRAS ADN

»  ANÁLISIS DE GENOMAS
     ANÁLISIS DE GENOMAS
     ONTOLOGÍA
     IDENTIFICACIÓN TRANSPOSONES
   

»  ANÁLISIS DE PROTEÍNAS
     COMPOSICIÓN Y PROPIEDADES QUÍMICAS
     COMPARACIÓN DE SECUENCIAS
     PREDICCIÓN DE ESTRUCTURA
     DETECCIÓN DE MOTIVOS PROTEICOS
     PREDICCIÓN DE LOCALIZACION CELULAR
     PREDICCIÓN DE INTERACCIONES
     MODIFICACIONES POSTRADUCCIONALES
     OTRAS

»  FILOGENIA

»  ANÁLISIS DEL ARN   
      PLEGAMIENTOS, ESTRUCTURA
      RNA RIBOSOMAL
      siRNA
      PSEUDOKNOTS
      tRNA
»  ANÁLISIS DEL TRANSCRIPTOMA
     ANÁLISIS Y VISUALIZACION
     MICROARRAYS
     MPSS

»  ANÁLISIS DEL PROTEÓMA

»  ANÁLISIS DE CARBOHIDRATOS

»  ANÁLISIS DEL METABOLISMO

»  OTRAS HERRAMIENTAS
     CÁLCULO DE PCR
     SOLUCIONES TAMPÓN

     CENTRIFUGACIÓN
     CALCULADORA

»  PROGRAMAS BIOINFORMÁTICA

INICIO


BÚSQUEDA DE SECUENCIAS

BLASTN
Búsqueda de secuencias de ADN basada en secuencias de ADN BLAST (NCBI)
BLAST (EBI)
BLAST (I Pasteur)
BLAST (Gramene)
BLAST (EMBnet)
BLAST (Expasy)
BLASTP BLASTP  (NCBI)
BLASTP (GTOP)
WU-BLAST To find regions of sequence similarity quickly, with minimum loss of sensitivity. WU-BLAST
PSI-BLAST Position-Specific Iterative BLAST creates a profile after the initial search.  This is used subsequent searches. PSI-BLAST
PHI-BLAST Position-Specific Iterative BLAST creates a profile after the initial search.  This is used subsequent searches. PHI-BLAST
BLASTX Translated BLAST BLASTX
TBLASTN Searches translated nucleotide databases using a protein query. TBLASTN
TBLASTX Searches translated nucleotide databases using a translated nucleotide query TBLASTX
SIB-BLAST Check the potential homologs SIB-BLAST
Scans the transport protein database (TC-DB) producing alignments and phylogenetic trees. TC-BLAST
Batch BLAST Permite enviar un archivo que contiene varias secuencias y luego organizar los resultados por cada secuencia individualmente Batch BLAST
FASTA Búsqueda basada en comparación de secuencias FASTA (EBI)
FASTA (DDBJ)
FASTA (U.Virginia)
Fasta33
Par Align Similitud de secuencia rápida y sensible ParAlign


COMPASS
Extracts protein sequences after ORF prediction and subsequently performs an automatic analysis for each of the proteins including BLASTp, FASTA and Pfam. STORM


ANÁLISIS DEL ADN

MANIPULACIÓN DE SECUENCIAS DE ADN
ARRIBA
        CAMBIOS DE FORMATO
Sequence editor Contiene numerosas aplicaciones para cambiar el formato de las secuencias
fmtseq  Aplicaciones para cambiar el formato de las secuencias
Readseq Cambio del formato de una secuencia
CLEANER Stripping off nonsequence material (e.g. numbers) from nucleic acid and protein sequence.
Nucleic Acid Sequence Massager Elimina las partes "no-secuencia" (por ejemplo, números) de la secuencia de ácido nucleico o proteína.
gbk2ptt Convierte de GenBank flat file (*.gbk) a NCBI Protein Table (*.ptt) file.
gbk2faa Convierte de GenBank flat file (*.gbk) a FASTA file incluyendo las regiones codificantes traducidas a aminoácidos.
gbk2fna Convierte de GenBank flat file (*.gbk) a FASTA file (*.fna)
gbk2ffn Extrae de un GenBank flat file (*.gbk) las secuencias de ADN de cada gen y las presenta en FASTA format (*.ffn)
gbk2sqn Convierte un GenBank flat file (*.gbk) a NCBI Sequin submission (*.sqn) file. 
Convert GenBank to Fasta Convierte secuencias en GenBank flat file (*.gbk) a FASTA file.
FeatureExtract Extracts sequence and feature annotation, such as intron/exon structure, from GenBank entries and other GenBank format files.
Extrae de
las entradas GenBank y otros archivos en formato GenBank la secuencia, anotación de función, estructura de intrón / exón, etc
PlasmaDNA Múltiples herramientas para ayudar en el diseño de una estrategia de clonación, generación de las secuencias de los nuevos clones, y archivar la estrategia de la clonación.

        INVERSION Y COMPLEMENTACIÓN

DNA Sequence Reverse and Complement Inversión y complementación de una secuencia de ADN
REVSEQ Inversión y complementación de una secuencia de ADN
Reverse-Complement Inversión y complementación de una secuencia de ADN
Reverse, Complement, Inverse Inversión y complementación de una secuencia de ADN
Reverse Complement of Sequence Inversión y complementación de una secuencia de ADN
Reverse complement Inversión y complementación de una secuencia de ADN
Reverse complement Inversión y complementación de una secuencia de ADN
Reverse complement Inversión y complementación de una secuencia de ADN
Reverse complement Inversión y complementación de una secuencia de ADN
Reverse complement Inversión y complementación de una secuencia de ADN
Reverse complement Inversión y complementación de una secuencia de ADN

        GENERACIÓN DE SECUENCIAS AL AZAR
Sequencing Shuffling Mezcla la secuencia de una proteína o ácido nucleico para producir una secuencia al azar con la composición general igual que la secuencia original.
Shuffle Baraja aleatoriamente una secuencia de ADN
Sequence Randomizer Crea secuencias al azar

         REPRESENTACIÓN GRÁFICA DE ADN
ApE Plasmid Editor Dibuja mapas y gráficos que utilizan las anotaciones de los archivos de GenBank y EMBL, crea  mapas de restricción lineales o circulares con las características indicadas y permite realizar análisis BLAST, junto con un número de otras características útiles. Requiere instalación.
pDRAW32 Permite introducir las coordenadas de los elementos genéticos, tales como los genes, que se representan en las secuencias de ADN. Requiere instalación.
Plasmid Processor Representación gráfica de plásmidos y secuencias lineales. Requiere instalación.
Sequence Extractor Genera mapas de restricción clicables y mapas de PCR de una secuencia de ADN, traducción de proteínas, divisones intrón / exón. 

                   COMPOSICIÓN                    
ARRIBA
WORDCOUNT GEMS Calcula la composición en nucleótidos, dinucleótidos, etc.
Z curve Calcula curvas Za partir de secuencuas de ADN
DNA base composition analysis tool Calcula el porcentaje de nucleótidos o dinucleótidos , la distribución de nucleótidos, y el sesgo acumulado  para una secuencia determinada. El resultado se puede mostrar en gráficos y datos.
Graphe:ADN riche en Representación gráfica de la riqueza en AT o GC
GenSkew Representación gráfica de la riqueza en un o varios nucleótidos a lo largo de una secuencia.
REPFIND Representación gráfica y estadística de la presencia de repeticiones directas en una secuencia.
DNA sequence Estadísticas de una secuencia de ADN.

TRADUCCIÓN

ARRIBA
       TRADUCCIÓN DIRECTA (DNA A PROTEÍNA)
MBS Translator Traducción DNA a proteína
DNA Analyzer Traducción DNA a proteína
ExPASy Traducción DNA a proteína
Translate Nucleic Acid Sequence Tool Traducción DNA a proteína
Virtual Ribosome Traducción de múltiples secuencias
Translate Traducción DNA a proteína
AiO Conjunto de aplicaciones para la edición y análisis de secuencias. Requiere instalación
(Reverse)-Transcription and Translation  Traducción directa y reversa de una secuencia

       
TRADUCCIÓN REVERSA (PROTEÍNA A DNA)

RevTrans 1.4 Server RevTrans toma un conjunto de secuencias de ADN, las traduce y alinea las secuencias peptídicas, y lo utiliza como base para la construcción del  correspondiente alineamiento múltiple de ADN.
Reverse Translate Traducción reversa de una secuencia
(Reverse)-Transcription and Translation  Traducción directa y reversa de una secuencia
Reverse Translate Traducción reversa de una secuencia
Protein backtranslation Traducción reversa de una secuencia
AiO Conjunto de aplicaciones para la edición y análisis de secuencias. Requiere instalación

RESTRICCIÓN
ARRIBA
NEBcutter V2.0 Encuentra los ORFs y los sitios de corte de los enzimas de restricción
Webcutter 2.0 Encuentra los sitios de corte de los enzimas de restricción
WatCut Encuentra los sitios de corte de los enzimas de restricción
Restriction Site Analysis Encuentra los sitios de corte de los enzimas de restricción
tacg V3.5 Encuentra los sitios de corte de los enzimas de restricción
Restenzyme Encuentra los sitios de corte de los enzimas de restricción
RESTRICT Encuentra los sitios de corte de los enzimas de restricción
Restriction Mapper Encuentra los sitios de corte de los enzimas de restricción
Sequence Extractor Sitúa los sitios de corte de los enzimas de restricción y los lugares de unión de primers
Restriction Enzyme Picker Encuentra grupos de 4 endonucleasas de restricción disponibles comercialmente que diferencian inequívocamente una secuencia de un grupo de secuencias para el uso como T-RFLP.
MB DNA Analysis Numerosas aplicaciones para el análisis de secuencias. Requiere instalación.
SEQtools Numerosas aplicaciones para el análisis de secuencias. Requiere instalación.
WinGene Numerosas aplicaciones para el análisis de secuencias. Requiere instalación.
GENtle Numerosas aplicaciones para el análisis de secuencias. Requiere instalación.
ApE Plasmid Editor Mapas de restricción y representación gráfica de secuencias. Requiere instalación.
AiO Numerosas aplicaciones para el análisis de secuencias. Requiere instalación.
DNA sequence Encuentra los sitios de corte de los enzimas de restricción
- - -
DISEÑO DE OLIGOS
ARRIBA
Primer3
Diseño de primers para PCR
Primer3Plus Diseño de primers para PCR
GeneFisher Interactive PCR Primer Design
PCR Now Created to design Real-Time Polymerase Chain Reaction (RT-PCR) primers for any number of user-defined coding sequences.
Primer-BLAST Developed at NCBI to help users make primers that are specific  to the input PCR template.
JOG 1.01 Javascript Oligonucleotide Generato
PCR primer selection
RAPD-primer generator
FastPCR Design of PCR primers for any aplication
CODEHOP COnsensus-DEgenerate Hybrid Oligonucleotide Primers used to design primers based upon multiple sequence alignments.
Primaclade Accepts a multiple species nucleotide alignment file as input and identifies a set of PCR primers that will bind across the alignment.
PriFi Upload a file containing Fasta-formatted DNA sequences or alternatively a *.aln file, select the control one  wants over the primer design from an extensive list and press "Find primers in alignment."
Primer3: WWW primer tool A very powerful PCR primer design program permitting one considerable control over the nature of the primers, including size of product desired, primer size and Tm range, and presence/absence of a 3’-GC clamp.
GeneFisher - Interactive PCR Primer Design A site allowing great control over primer design.
PCR Now Created to design Real-Time Polymerase Chain Reaction (RT-PCR) primers for any number of user-defined coding sequences.
cDNA_Primers Designs primers around open reading frames.
SNP_Primers Designs primers around every SNP in a GenBank file.
Genomic_Primers Designs primers around exons in genomic sequence. All you need is a GenBank file containing your  gene.
Overlapping_Primers Creates multiple overlapping PCR products in one sequence.
MuPlex Multi-objective multiplex PCR assay design - designed for large-scale multiplex PCR assay design in an automated high-throughput environment, where high coverage is required.
eprimer3 Picks PCR primers and hybridization oligos

Picky

Oligo microarray design program that identifies probes that are very unique and specific to input sequences.
GenomePrimer Provides a high-throughput method to select, with minimal user intervention and maximum flexibility, the most unique regions within DNA sequences and design primers that meet certain preset criteria.
AiO Combines typical DNA/protein features such as plasmid map drawing, finding of ORFs, translate, backtranslate, primer design and virtual cloning.
Fast PCR Design PCR primers, alignment and repeat sequence searching.
Oligo Explorer A tool to search primers and primer pairs.
AnnHyb Sequence  editing with proofreading, format conversion, translation, sequence statistics, probe design & analysis. 
RealTimeDesign
QuantPrime Reliable primer design for use in larger qPCR experiments.
 Real-time PCR (TaqMan) Primer Design
WatCut Takes an oligonucleotide and introduces silent mutations in potential restriction sites such that the amino acid sequence of the protein is unaltered. 

CALCULO DE LA Tm DE PRIMERS Y SONDAS

ARRIBA
OligoCalc Oligonucleotide properties calculator
Poland Tm calculator
Tm for an oligo
NetPrimer Tm, thermodynamic properties and most stable hairpin & dimers.
dnaMATE Calculates a consensus Tm) for short DNA sequence (16-30 nts)
OligoAnalyzer Hairpin, self-dimer analysis, BLAST the sequence against NCBI's database and measure the impact of incorporating 5'-modifications into the sequence.
Oligonucleotide Properties Calculator Also permits analysis of  6-FAM, HEX, or TAMRA-labelled oligos. 
Biopolymer Calculator
Melting Enthalopy, entropy and melting temperature
DAN For a complete picture of your sequence change "window size" to the size of your fragment, change "shift increment" to zero, and click on "Produce a plot"
Hybridization of two different strands of DNA or RNA Computations consider 5 different ensembles of structures. Partition function calculations are performed for the heterodimer, the two possible homodimers, and for folding of both single strand. Ensemble free energies are computed, leading to simulation of heat capacity, Cp, as a function of temperature. Base pair probabilities are computed and combined with published extinction coefficients to simulate UV absorbance as a function of temperature.
Homodimer simulations This simulation considers both the folding and dimerization of one single-stranded DNA or RNA molecule.
DINAMelt Nucleic acid melting prediction
MELTING Enthalpie, entropy and melting temperature
Poland
Oligo Tm
Oligo Tm
Stitchprofiles.uio.no Analysis of partly melted DNA conformations using stitch profiles
AutoDimer Screen previously selected PCR primers for primer-dimer and hairpin interactions.
Oligo Analyzer To determine primer properties like Tm, GC%, primer loops, primer dimers and primer-primer compatibility.
MeltCalc Allows you to analyze probes.

ALINEAMIENTO DE 2 SECUENCIAS
ARRIBA
LALIGN
LalnView Graphical program for visualizing local alignments between two sequences

BLAST2 - Pasteur Institute (France)

BLAST2 - EMBL (Germany)

COMPBLAST - TigemNet (Italy)

BLAST2 - ExPasy (Switzerland) 

BLAST2 - Compugen (US/Israel)
BLAST2 - NCBI (US)

ALINEAMIENTO MÚLTIPLE
ARRIBA
MultAlin Multiple sequence alignment
Multiple Alignment Multiple sequence alignment
ClustalW Multiple sequence alignment (<30 seq)
ClustalW-XXL Multiple sequence alignment (>30 seq)
ClustalX Multiple sequence alignment
BioEdit Sequence alignment editor

CLUSTERING
ARRIBA
CAP (Italy) Ensamblado de secuencias cortas
CAP3 (Lyon) Ensamblado de secuencias cortas
CAP3 (Infobiogen) Ensamblado de secuencias cortas
CAP3 (PBIL, France) Ensamblado de secuencias cortas
CAP (FIRC, Italy) Ensamblado de secuencias cortas

VECTORES

ARRIBA
CloneIt! Finding sub-cloning strategies, in-frame deletions and frameshift using restriction enzymes and DNA polymerase.
VecScreen Screens your DNA sequence for potential vector sequence.

DETECCIÓN DE GENES
ARRIBA
ORF Finder
ORF Predicts ORFs in a FASTA input DNA sequence
GeneMark A family of programs for ORF analysis. 
Gene Identification
FramePlot 2.3 ORF detection
Third Position GC Skew Display Predicts genes by comparing possible open reading frames to a third position GC plot.
GENIO/frame Detección de errores de secuenciación en ORFs
FrameD Identifica posibles genes en una secuencia

DETECCIÓN DE MOTIVOS DE ADN

ARRIBA
Rfam Analyze 2 kb of DNA for 36 structural or functional RNAs such as 5S rRNA, tRNA, tmRNA, group I & II catalytic introns, hammerhead ribozymes, signal recognition particles.
WebLogo Graphical way of representing and visualizing consensus sequence data
RNA Structure Logo Graphical way of representing and visualizing consensus sequence data
Motif Sampler To find over-represented motifs (cis-acting regulatory elements) in the upstream region of a set of co- regulated genes.
SCOPE To identifying novel cis-regulatory elements from groups of upstream sequences.
TICO Translation Initiation site COrrection - provides an interface for direct post processing of the predictions obtained from GLIMMER to improve the accuracy of annotated Translation Initiation Sites
TransTerm Sarches for rho-independent terminators in the vicinity of annotated genes.

METILACIÓN

ARRIBA
MethPrimer Design Primers for Methylation PCRs
Bisulfite Genomic DNA Sequencing For analysis of plant DNA methylation
Bisulfite Genomic Sequencing
Bisulfite Sequencing of Small DNA/Cell Samples

OTRAS ADN
ARRIBA
DSHIFT Predicting DNA 1H, 13C & 31P chemical shifts




ANÁLISIS DE GENOMAS
ARRIBA
Gene Context Tool Visualizing the genome context of a gene or group of genes (synteny).
Genome Analysis Pipeline

Saccharomyces genome analysis.

Genome Analysis Pipeline

Higher eukaryotes genome analysis

ONTOLOGÍA
ARRIBA
GOAnno Automatically annotates proteins according to the Gene Ontology using hierarchised multiple alignments.

IDENTIFICACIÓN DE TRANSPOSONES
ARRIBA
REPuter Computation of maximal repeats in complete genomes
LTR_FINDER Finding LTR retrotransposons in genomes
RT Analizer Finding new retrotransposons and detecting L1 retrotransposition signatures
REPATT & TRANSPO Search tools for transposable elements


ANÁLISIS DE PROTEÍNAS

COMPOSICIÓN Y PROPIEDADES QUÍMICAS
ARRIBA
ProtParam tool Amino acid composition & Mass
Compute pI/Mw tool
ProteinChemist Plot of the relationship between charge and pH
JVirGel Proteomic Tools Plot of the relationship between charge and pH
PEPSTATS Mass, pI, composition and mol% acidic, basic, aromatic, polar etc. amino acids
Biochemistry-online % composition, molecular weight, pI, and charge at any desired pH.
Protein calculator Calculates mass, pI, charge at a given pH, counts amino acid residues etc.
GoCore "Microsoft  Excel"-based bioinformatics tool for protein sequence analysis. 
   
COMPARACIÓN DE SECUENCIAS
ARRIBA
SIM Alignment tool for protein. The results  can be visualized best with LALIGNVIEW.
Secondary Structure Computes alignments of protein secondary structures.
 Element Alignment Computes alignments of protein secondary structures.
ClustalW (EBI) Multiple Sequence Alignment
ClustalW (I Pasteur) Multiple Sequence Alignment
ClustalW (EMBL) Multiple Sequence Alignment
ParAlign Sequence alignment.
BLAST 2


PREDICCIÓN DE ESTRUCTURA
ARRIBA
PQS Protein Quaternary Structure
Coils To screen for coiled-coil regions in proteins 
Paircoils To screen for coiled-coil regions in proteins 
MultiCoil To screen for coiled-coil regions in proteins 

DETECCIÓN DE MOTIVOS PROTÉICOS
ARRIBA
The MEME Suite Motif-based sequence analysis tools
MEME Multiple EM for Motif Elicitation
GLAM2 Gapped Local Alignments of Motifs
Block Maker Finds conserved blocks in a group of two or more unaligned related protein sequences.
WebLogo Graphical way of representing and visualizing consensus sequence data
MOTIF
Pfam 
ScanProsite
Block Searcher
SMART Searches sequence for the domains/ sequences listed in the homepage.
MEROPS BLAST Permits one to screen protein sequences against an extensive database of characterized peptidases

PREDICCIÓN DE LOCALIZACIÓN CELULAR
ARRIBA
TMpred  Prediction of Trans-membrane Regions and Orientation
TMHMM Prediction of transmembrane helices in proteins
DAS Transmembrane Prediction Server
SPLIT Transmembrane Protein Topology Prediction Server
OCTOPUS
Phobius Transmembrane Protein Topology Prediction Server
SPOCTOPUS  Transmembrane Protein Topology Prediction Server
RHYTHM Predicts the orientation of transmembrane helices in channels and membrane-coils,

PREDICCIÓN DE INTERACCIONES
ARRIBA
MolSurfer A program which can be used to study protein-protein and protein-DNA/RNA interfaces.  The 2D projections of the computed interface aid visualization of complicated interfacial geometries in 3D. Molecular properties, including  hydrophobicity and electrostatic potential, can be projected onto the interface. MolSurfer can thereby aid exploration of molecular complementarity, identification of binding "hot spots" and prediction of the effects of mutations. MolSurfer can also facilitate the location of cavities at macromolecular interfaces.
Antibody Design Antigenicity and Allergenicity prediction
Abie Pro Peptide  Antigenicity and Allergenicity prediction
EVALLER Antigenicity and Allergenicity prediction
SBS EpiToolKit Antigenicity and Allergenicity prediction
Antigenicity Plot Computes and plots the antigenicity along the polypeptide chain
Antigenicity Prediction Find antigenic sequences and also reviews them from the point of hydrophobicity and aggregation
EMBOSS Antigenic Predicts potentially antigenic regions of a protein sequence
EMBOSS Antigenic Predicts potentially antigenic regions of a protein sequence

MODIFICACIONES POST-TRADUCCIONALES

ARRIBA
PeptideCutter Predicts cleavage sites for enzymes and chemicals.
Mobility_plot 4.1 Predicts cleavage sites for enzymes and chemicals.
FindMod tool To predict potential protein post-translational modifications in peptides
GlycoMod Tool Predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses

OTRAS
ARRIBA
GoCore "Grouping of Conserved regions" is a "Microsoft  Excel"-based bioinformatics tool for protein sequence analysis. 


FILOGENIA
Phylip on the Web A package of programs for inferring phylogenies. 
PHYLIP A package of programs for inferring phylogenies. 
Phylogeny.fr To reconstructing and analysing phylogenetic relationships between molecular sequences.It includes multiple alignment (MUSCLE, T-Coffee, ClustalW, ProbCons), phylogeny (PhyML, MrBayes, TNT, BioNJ), tree viewer (Drawgram, Drawtree, ATV) and utility programs (e.g. Gblocks to eliminate poorly aligned positions and divergent regions)
HyPhy To perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses.
TREECON A software package developed primarily for the construction and drawing of phylogenetic trees on the basis of evolutionary distances inferred from nucleic and amino acid sequences.
TREEMAP A simple tool for visually comparing host and parasite phylogenies: you can view the host and parasite trees, interactively create reconstructions of the history of the host-parasite association, perform randomization tests of tree similarity, and (if you have branch length information such as might be obtained from DNA sequence data) compare branch lengths in the two trees. 
Treefinder Computes phylogenetic trees from nucleotide sequences. Using the widely accepted Maximum Likelihood method
PopG Simulates evolution of a single locus in the presence of natural selection, mutation, migration, and genetic drift. 
MEGA Phylogenetic analysis program.
TreeExplorer
Tree-Puzzle Constructs phylogenetic trees from molecular sequence data by maximum likelihood.
Modeltest Uses hierarchical likelihood ratio tests (hLRT) to compare the fit of the nested GTR (General Time Reversible) family of nucleotide substitution models. Additionally, it calculates the Akaike Information Criterion estimate associated with the likelihood scores.
TreeView Provides a simple way to view the contents of a NEXUS, PHYLIP, or other format tree file
GeneTree Comparing gene and species trees.
MrBayes A program for Bayesian inference of phylogeny using Markov Chain Monte Carlo methods.
CERVUS Parentage analysis using a likelihood approach.
ProSeq A program for convenient sequence alignment editing and various population-genetic analyses.
PAML A program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
TipDate A program to estimate the rate of molecular evolution and time-scale of a phylogeny from dated sequences.
NJplot A tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format





ANÁLISIS DEL ARN
PLEGAMIENTOS, ESTRUCTURA
ARRIBA
 tRNAscan-SE Provides secondary structure  diagrams of the tRNA molecules.
ARAGORN Provides secondary structure  diagrams of the tRNA molecules.
FindtRNA Provides secondary structure  diagrams of the tRNA molecules.
TFAM Predict tRNA Secondary Structures
BRUCE Detects transfer-messenger RNAs which function to free ribosome-stalled mRNAs.
MARNA Multiple Alignment of RNAs
FOLDALIGN Folds and aligns RNA structures
MFold RNA folding
Vienna RNA secondary structure prediction For drawing tRNAs in cloverleaf format.
CONTRAfold Secondary structure prediction
Radar Provides constrained alignment of RNA secondary structures, and prediction of the consensus structure for a set of RNA sequences.

RNA RIBOSOMAL
ARRIBA
Ribosomal RNA BLAST BLASTN against the SSU (16S) and LSU (23S) rRNA databases;  and a quick phylogeny search.
Rifle Compares restriction patterns of 16S rDNA amplicons against a database of theoretical restriction

siRNA
ARRIBA
SiRNA Selector Scans a target gene for candidate siRNA sequences that satisfy user-adjustable rules.
siRNA Target Designer Scans a target gene for candidate siRNA sequences that satisfy user-adjustable rules.
siRNA Target Finder Scans a target gene for candidate siRNA sequences that satisfy user-adjustable rules.
siRNA Target Finder Scans a target gene for candidate siRNA sequences that satisfy user-adjustable rules.
siRNA Design Software Scans a target gene for candidate siRNA sequences that satisfy user-adjustable rules.

PSEUDOKNOTS
ARRIBA

tRNA
ARRIBA


ANÁLISIS DEL TRANSCRIPTOMA

ANÁLISIS Y VISUALIZACIÓN
ARRIBA
Expression Profiler A suite of tools for clustering, analysis and visualization of gene expression and other genomic data.To perform cluster analysis, pattern discovery, pattern visualization, study and search Gene Ontology categories, generate sequence logos, extract regulatory sequences, study protein interactions, as well as to link analysis results to external tools and databases.
EPCLUST Expression Profile data CLUSTering and analysis. A tool for expression data matrix handling and visualization
SPEXS  Sequence Pattern EXhaustive Search, a sequence pattern discovery tool 
SEQLOGO  Sequence logo drawing tool 
GEPAS Gene Expression Pattern Analysis Suite - An experiment-oriented pipeline for the analysis of microarray gene expression data. It contains an incredible number of tools for normalization, preprocessing, viewing, clustering, differential expression, supervised classification, and data mining & analysis.
Cyber-T

MICROARRAYS
ARRIBA
DNA arrays Proprocessing, viewers, unsupervised clustering, differential gene expression, supervised classification, and data mining modules.
M@CBETH MicroArray Classification Benchmarking Tool on Host server
NIA Array Analysis Tool
VAMPIRE microarray analysis suite
MicroArray Genome Imaging & Clustering Tool
MIDAW MIcroarray Data Analysis Web tool
GEMS Gene Expression Mining Server

MPSS
ARRIBA




ANÁLISIS DEL PROTEOMA
ARRIBA
Gelprint Generates an in silico 2D-gel from the theoretical pI (isoelectric point) and Mw (molecular weight) data for a set of proteins.
Virtual Two-Dimensional Protein Gels
FLICKER For comparing images, such as two 2-D gels from different Internet sources on your Web browser.


ANÁLISIS DE CARBOHIDRATOS
ARRIBA
Sweet For constructing 3D models of saccharides from their sequences.
GLYCAM Biomolecular Builder To elucidate the conformational properties of oligosaccharides
CSS Carbohydrate Structure Suite : analysis of carbohydrate 3D structures derived from the PDB


ANÁLISIS DEL METABOLISMO
ARRIBA


OTRAS HERRAMIENTAS
ARRIBA
Electrophoresis simulation Proteins.
Secret Coder Tool To encode secret messages in DNA sequence.

CÁLCULO DE PCR
ARRIBA
PCR Box Titration Calculator For figuring out the amounts of each reagent to use in a two-dimensional box titration for PCR. 
PCR Reaction Mixture Setup

SOLUCIONES TAMPÓN
ARRIBA
JaMBW Buffer Calculator (chapter 5)
Biological buffer calculator Controls for concentration, ionic strength and temperature.
Phosphate Buffer Calculation Calculates the amount of monosodium phosphate and trisodium phosphate necessary to achieve a buffer with a given pH and strength.
Dilution Calculator

CENTRIFUGACIÓN
ARRIBA
Centrifuge Helper Provides one with maximum RPM, RCF (ave, min, max), K factor and comparison between two rotors
Centrifuge Rotor Speed Calculator

CALCULADORA CIENTÍFICA
ARRIBA
Physical mapping calculator - library construction The number of clones required to cover the DNA
Radioactive Decay Calculator
Radioactive Decay Calculator
Calculations Spectrophotometric measurement of nucleic acids concentration; Conversion: speed of rotation [krpm] - Relative Centrifuge Force [kg];
BioMath Calculators



PROGRAMAS BIOINFORMÁTICA
ARRIBA
2can Bioinformatics (EBI)