Lista de Ferramentas de Bioinformática
(Diferença entre revisões)
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=Análise de sequências= | =Análise de sequências= | ||
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*[http://www.codoncode.com/ CodonCode Aligner] | *[http://www.codoncode.com/ CodonCode Aligner] | ||
:CodonCode Aligner is an easy-to-use program for sequence assembly, contig editing, and mutation detection. | :CodonCode Aligner is an easy-to-use program for sequence assembly, contig editing, and mutation detection. | ||
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=Alinhamento de sequências= | =Alinhamento de sequências= | ||
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*[http://clovr.org/category/blog/ CloVR] | *[http://clovr.org/category/blog/ CloVR] | ||
:Automated Sequence Analysis from Your Desktop | :Automated Sequence Analysis from Your Desktop | ||
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+ | =ORGANIZAR ASAP= | ||
+ | *[http://www.expasy.org/ Expert Protein Analysis System] | ||
+ | :ExPASy is the new SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences | ||
+ | |||
+ | *[http://img.jgi.doe.gov/ Integrated Microbial Genomes System] | ||
+ | :The Integrated Microbial Genomes (IMG) is a genome browsing and annotation system | ||
+ | |||
+ | *[http://gmod.org/wiki/Main_Page GMOD] | ||
+ | :GMOD is the Generic Model Organism Database project, a collection of open source software tools for creating and managing genome-scale biological databases | ||
+ | |||
+ | *[http://inismor.ucd.ie/%7Etalign/index.html t-Align] | ||
+ | :Compara réplicas de T-RFLP | ||
+ | |||
+ | *[http://www.sanger.ac.uk/resources/software/artemis/ Artemis] | ||
+ | :Artemis is a free genome browser and annotation tool that allows visualisation of sequence features | ||
+ | |||
+ | *[http://www.ecoevol.ufg.br/sam/ Spatial Analisys in Macroecology] | ||
+ | :SAM (Spatial Analysis in Macroecology) is a program designed as a package of tools for spatial statistical analysis, mainly for applications in Surface Pattern Spatial Analysis. | ||
+ | |||
+ | *[http://david.abcc.ncifcrf.gov/ David] | ||
+ | :Database for Annotation, Visualization and Integrated Discovery (DAVID ) | ||
+ | |||
+ | *[http://blip.codeplex.com/ BL!P: BLAST in Pivot] | ||
+ | :BL!P is a computer program that automates the NCBI BLAST alignment of coding DNA or protein sequences and processes the results for visualization in the Microsoft Live Labs program Pivot. | ||
+ | |||
+ | *[http://www.ab.wur.nl/Cyrille2 Cyrille2 - Cyrille2 Wiki] | ||
+ | :Cyrille2 is a system to operate high-throughput pipelines in bioinformatics. | ||
+ | |||
+ | *[http://ged.msu.edu/angus/index.html Angus 2.0] | ||
+ | :ANGUS is a site built around the 2010 course on Analyzing Next-Generation Sequencing Data. It contains a number of detailed tutorials on mapping, assembly, mRNAseq, ChIP-seq, and resequencing analysis. | ||
+ | |||
+ | *[http://www.encyclon.net/multiblast/MultiBlastX.htm MultiBlastX] | ||
+ | :compares a nucleotide query sequence translated in all reading frames against a protein sequence database | ||
+ | |||
+ | *[http://bioinformatics.unc.edu/software/opensource/index.htm UNC OpenSource Software list] | ||
+ | :Lista de Ferramentas | ||
+ | |||
+ | *[http://en.wikipedia.org/wiki/Category:Bioinformatics_software Wikipedia Bioinformatics] | ||
+ | :Bioinformatics Software | ||
+ | |||
+ | |||
+ | |||
+ | === Idaho University - IBEST Applications (home brew!) === | ||
+ | |||
+ | *MiCA [http://mica.ibest.uidaho.edu/ Microbial Community Analysis] | ||
+ | *HiTSA [http://www.ibest.uidaho.edu/tools/hitsa/index.php High Throughput Sequence Analysis] | ||
+ | *Statgen [http://www.ibest.uidaho.edu/tools/statgen/index.php Genetic Distances Statistical Generator] | ||
+ | |||
+ | === Phylogenetic Congruence === | ||
+ | * [http://rogerlab.biochemistryandmolecularbiology.dal.ca/Software/Software.htm#Concaterpillar concaterpillar] | ||
+ | |||
+ | === Phylogenetic Inference === | ||
+ | |||
+ | * [http://geta.life.uiuc.edu/%7Egary/programs/fastDNAml/fastDNAml_1.2.2/docs/fastDNAml_doc_1.2.txt FastDNAml] | ||
+ | * [https://www.nescent.org/wg_garli/Main_Page Garli] | ||
+ | * [http://www.stats.ox.ac.uk/%7Egriff/gtree.doc GeneTree] | ||
+ | * [http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/manual.html Mesquite] | ||
+ | * [http://www.ibest.uidaho.edu/help/%20bioapps//Modeltest3.06.pdf ModelTest] | ||
+ | * [http://mrbayes.csit.fsu.edu/ MrBayes] | ||
+ | * [http://www.nhm.ac.uk/research-curation/projects/software/p4.html P4] | ||
+ | * [http://abacus.gene.ucl.ac.uk/software/pamlDOC.pdf PAML] | ||
+ | * [[PAUP]] | ||
+ | * [http://evolve.zoo.ox.ac.uk/ Seq-Gen] | ||
+ | * [[Phylip]] | ||
+ | * [http://atgc.lirmm.fr/phyml/ Phyml] | ||
+ | * [http://icwww.epfl.ch/~stamatak/index-Dateien/countManual7.0.4.php RAxML] | ||
+ | * [http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm RAxML web] | ||
+ | * [http://taxonomy.zoology.gla.ac.uk/rod/treeview/treeview_manual.html TreeView] | ||
+ | * [http://beast.bio.ed.ac.uk/Main_Page BEAST] | ||
+ | |||
+ | === Population Genetics === | ||
+ | |||
+ | * [http://www.math.wustl.edu/%7Esawyer/geneconv/gconvdoc.html GeneConv] | ||
+ | * [http://evolution.genetics.washington.edu/lamarc/fluctuate.html Fluctuate] | ||
+ | * [http://evolution.genetics.washington.edu/lamarc/index.html Lamarc] | ||
+ | * [http://popgen.csit.fsu.edu/ Migrate] | ||
+ | * [http://evolution.genetics.washington.edu/lamarc/recombine.html Recombine] | ||
+ | * [http://pritch.bsd.uchicago.edu/structure.html Structure] | ||
+ | * [http://genfaculty.rutgers.edu/hey/software IM and IMA] | ||
+ | |||
+ | ===Misc=== | ||
+ | * [http://www.girinst.org/repbase/index.html RepBase] | ||
+ | * R8 | ||
+ | * [http://emboss.sourceforge.net/docs/adminguide/node65.html Cutg] | ||
+ | * [http://www.ncbi.nlm.nih.gov/IEB/ToolBox/index.cgi NCBI Toolkit] | ||
+ | * [http://rebase.neb.com/rebase/rebase.html Rebase] | ||
+ | * Wise | ||
+ | * [http://bobcat.genomecenter.ucdavis.edu/mediawiki/index.php/STAP_download Stap] | ||
+ | * Oomf | ||
+ | * [http://emboss.sourceforge.net/embassy/ Embassy] | ||
+ | * [http://genfaculty.rutgers.edu/hey/software IM] | ||
+ | * [http://nmr.cit.nih.gov/xplor-nih/doc/current/ Xplor-NIH] | ||
+ | * [http://www.mpiblast.org/ Mpiblast] | ||
+ | * [http://www.plantpath.wisc.edu/fac/joh/dotur/documentation.html dotur] | ||
+ | |||
+ | =Cluster Tools= | ||
+ | *[http://ganglia.sourceforge.net/ Ganglia] | ||
+ | *[http://gridengine.sunsource.net/ SGE] | ||
+ | *[http://www.clusterresources.com/products/torque-resource-manager.php Torque/Maui] | ||
+ | *[http://www.open-mpi.org/ Openmpi] | ||
+ | *[http://www.mcs.anl.gov/research/projects/mpich2/ Mpich2] | ||
+ | *[http://www.lam-mpi.org/ Lam-mpi] | ||
+ | *[http://www.csm.ornl.gov/pvm/ PVM] | ||
+ | *[[Tutorials:_Using_modules_to_load_applications|Modules]] |
Edição de 13h17min de 26 de abril de 2012
Tabela de conteúdo |
Análise de sequências
Estrutura de Proteínas
Aplicativos Online
Aplicativos Standalone
- CodonCode Aligner is an easy-to-use program for sequence assembly, contig editing, and mutation detection.
Alinhamento de sequências
Aplicativos Online
- NCBI Basic Local Alignment Search Tool
- Bioinformatics Tools for Sequence Similarity & Analysis Searching
- Predição de estruturas protéicas 3D
- Ferramentas on-line de alinhamento e criação de árvores
- Interative Tree of Life
- Teste de modelos de alinhamento
Aplicativos Standalone
- Multiple alignment of nucleic acid and protein sequences
- MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses.
Contig Assembly
Bancos de Dados Biológicos
- Wiki com uma lista de banco de dados biológicos
- The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis.
- 2012 NAR Database Summary Paper Category List
Classificação e taxonomia
Aplicativos Online
- A prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species
Aplicativos Standalone
Análises Metagenômicas
- Metagenomic ORF finder
- Gene Prediction in Metagenomes and Novel Prokaryotes by Heuristic Approach
- LNCC Sabia Metagenomic tool
- Bioinformatics Lab (Labinfo) of the National Laboratory of Scientific Computation of the Ministry of Science and Technology (MCT) of Brazil
- This page contains information regarding the SEAStAR software tools referenced in our recent publication in Science: "Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota".
- Glimmer-MG is a system for finding genes in environmental shotgun DNA sequences.
- MEtaGenome ANalyzer
- Análises metagenômicas (necessita de sequencias anotadas)
- Software de anotação de sequências
- Serviço de anotação de sequências
- JCoast is a next-generation software solution for the exploration, mining and comparison of your genome and metagenome projects. Based on a set of predicted and automatically annotated ORFs (a genome or metagenome) it acts as a window into these preprocessed data which does not only allow to view the initial results but also facilitates improved annotation and in-depth data analysis.
- GenDB is a genome annotation system for prokaryotic genomes.
- The Metagenomics RAST (online)
- Portal for marine ecological genomics
- The GEBA project is aimed at systematically filling in the gaps in sequencing along the bacterial and archaeal branches of the tree of life.
- Integrated Microbial Genomes
- Naïve Bayesian Classification tool
- WebCARMA is a web-based system for the functional and taxonomic analysis of metagenomic DNA sequences.
- A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data
- Community Cyberinfrastructure for Advanced Microbial Ecology Research & Analysis
- IMG Metagenomics
- The greengenes web application provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading.
- Estimating Bacterial Composition from Metagenomic Sequences (linux)
- Ótimo framework com várias ferramentas online, como ORF_finder e fragGeneScan
- Orf finder tool
- Statistical Analysis of Metagenomic Profile
- An algorithm for taxonomic binning of metagenomic sequences Artigo
- DiScRIBinATE is a similarity based binning method.
- A high-performance computational pipeline for metagenomic data analysis
- Metastats: Detect Differentially Abundant Features
Análises Estatísticas
- Gromacs
- R
- The R Project for Statistical Computing
- RStudio™ is a new integrated development environment (IDE) for R.
Plataformas de Desenvolvimento
- BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl.
- Scripts em BioPerl
- NERC Scripts for Bioinformatics
- Learn Python The Hard Way, 2nd Edition
- Programming For Biologists
Blogs e Tutoriais
- QB3 Python Bioinformatics Course 2010
- NCBI RSS feed
- A personal blog about interesting news on the field of Bioinformatics, computational biology and related stuff
- Blogs de bioinformática
- biology as computational science
- Follow the conversation to learn how you can make the most of your data
- Open source bioinfomatics
- Computer science, bioinformatics, genetics, and everything in between
- As the title says, tips to learn R
- Do mesmos desenvolvedores do wikiPathways
- Science Youtube
- Bioinformatics Zen
- Aprendendo R
- Learn R
- Curso R
- Introdução à estatística básica com R
- Applied statistics for bioinformatics using R
- TINN-R
- GUI for R
- Diversos pacotes de análise Bioinformatica
Blog of Jonathan A. Eisen, evolutionary biologist, microbiologist and genomics researcher,
- Automated Sequence Analysis from Your Desktop
ORGANIZAR ASAP
- ExPASy is the new SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences
- The Integrated Microbial Genomes (IMG) is a genome browsing and annotation system
- GMOD is the Generic Model Organism Database project, a collection of open source software tools for creating and managing genome-scale biological databases
- Compara réplicas de T-RFLP
- Artemis is a free genome browser and annotation tool that allows visualisation of sequence features
- SAM (Spatial Analysis in Macroecology) is a program designed as a package of tools for spatial statistical analysis, mainly for applications in Surface Pattern Spatial Analysis.
- Database for Annotation, Visualization and Integrated Discovery (DAVID )
- BL!P is a computer program that automates the NCBI BLAST alignment of coding DNA or protein sequences and processes the results for visualization in the Microsoft Live Labs program Pivot.
- Cyrille2 is a system to operate high-throughput pipelines in bioinformatics.
- ANGUS is a site built around the 2010 course on Analyzing Next-Generation Sequencing Data. It contains a number of detailed tutorials on mapping, assembly, mRNAseq, ChIP-seq, and resequencing analysis.
- compares a nucleotide query sequence translated in all reading frames against a protein sequence database
- Lista de Ferramentas
- Bioinformatics Software
Idaho University - IBEST Applications (home brew!)
- MiCA Microbial Community Analysis
- HiTSA High Throughput Sequence Analysis
- Statgen Genetic Distances Statistical Generator
Phylogenetic Congruence
Phylogenetic Inference
- FastDNAml
- Garli
- GeneTree
- Mesquite
- ModelTest
- MrBayes
- P4
- PAML
- PAUP
- Seq-Gen
- Phylip
- Phyml
- RAxML
- RAxML web
- TreeView
- BEAST