Lista de Ferramentas de Bioinformática
De Lembiotech Wiki
(Diferença entre revisões)
(→Análises metagenômicas) |
(→Análise de sequências) |
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[[Categoria:Bioinformática]] | [[Categoria:Bioinformática]] | ||
| − | = | + | =Análise de sequências= |
| − | + | * [http://emboss.sourceforge.net/ EMBOSS] | |
| − | : | + | :A high-quality package of free, Open Source software for molecular biology |
| − | + | * [http://www.g-language.org/wiki/ G-Language] | |
| − | : | + | :G-language Genome Analysis Environment provides a greater variety of useful genome analysis tools compared to most existing analysis software packages, and is also easily pluggable. |
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| − | : | + | ===Estrutura de Proteínas=== |
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| − | : | + | * [http://styx.ibest.uidaho.edu/help/bioapps/amber7/amber7.pdf Amber7] |
| − | + | * [http://styx.ibest.uidaho.edu/help/bioapps/charmm/Charmm_3_0_Users_Guide.html Charmm] | |
| − | : | + | * [http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dtut.shtml Cn3d] |
| − | + | :Cn3D macromolecular structure viewer | |
| + | * [http://www.ks.uiuc.edu/Research/namd/ Namd] | ||
| + | :NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | ||
| + | * [http://www.umass.edu/microbio/rasmol/ Rasmol] | ||
| + | |||
| + | * [[Xplor]] | ||
| + | |||
| + | ==Aplicativos Online== | ||
| + | |||
| + | |||
| + | ==Aplicativos Standalone== | ||
| + | *[http://www.codoncode.com/ CodonCode Aligner] | ||
| + | :CodonCode Aligner is an easy-to-use program for sequence assembly, contig editing, and mutation detection. | ||
| + | |||
| + | =Alinhamento de sequências= | ||
| + | |||
| + | |||
| + | * [ftp://ftp.ncbi.nih.gov/blast/documents/ BLAST] | ||
| + | * [http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/Top.html ClustalW] | ||
| + | * [http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html ClustalX] | ||
| + | * [http://www.drive5.com/muscle/docs.htm Muscle] | ||
| + | * [http://www.megasoftware.net/index.html Mega] | ||
| + | * [http://www.psc.edu/general/software/packages/hmmer/manual/main.html HMMER] | ||
| + | * [http://mummer.sourceforge.net/ Mummer] | ||
| + | * [http://mafft.cbrc.jp/alignment/server/ MAFFT] | ||
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| + | |||
| + | ==Aplicativos Online== | ||
| + | *[http://blast.ncbi.nlm.nih.gov/Blast.cgi Blast NCBI Online] | ||
| + | :NCBI Basic Local Alignment Search Tool | ||
| + | |||
| + | *[http://www.ebi.ac.uk/Tools/similarityandanalysis.html Embl Tools] | ||
| + | :Bioinformatics Tools for Sequence Similarity & Analysis Searching | ||
| + | |||
| + | *[http://www.fundp.ac.be/sciences/biologie/urbm/bioinfo/esypred/ EsyPred3D] | ||
| + | :Predição de estruturas protéicas 3D | ||
| + | |||
| + | *[http://www.phylogeny.fr/version2_cgi/index.cgi Phylogeny.fr] | ||
:Ferramentas on-line de alinhamento e criação de árvores | :Ferramentas on-line de alinhamento e criação de árvores | ||
| − | + | ||
| + | *[http://itol.embl.de/index.shtml iTol] | ||
:Interative Tree of Life | :Interative Tree of Life | ||
| − | |||
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| + | *[http://darwin.uvigo.es/software/jmodeltest.html ModelTest] | ||
| + | :Teste de modelos de alinhamento | ||
| − | + | ==Aplicativos Standalone== | |
| − | + | *[http://www.clustal.org/ Clustal] | |
| − | + | :Multiple alignment of nucleic acid and protein sequences | |
| − | + | ||
| − | + | ||
| − | : | + | |
| − | + | *[http://www.megasoftware.net/ MEGA] | |
: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. | :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. | ||
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| + | === Contig Assembly === | ||
| + | * [http://www.phrap.org/phredphrapconsed.html Phred/Phrap/Consed] | ||
| + | * [http://www.repeatmasker.org/webrepeatmaskerhelp.html RepeatMasker] | ||
| + | * [http://seq.cs.iastate.edu/ Cap3] | ||
| − | + | ==Bancos de Dados Biológicos== | |
| − | : | + | *[http://en.wikipedia.org/wiki/List_of_biological_databases List of biological databases] |
| + | :Wiki com uma lista de banco de dados biológicos | ||
| + | *[http://www.arb-home.de/ ARB] | ||
| + | :The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. | ||
| − | + | *[http://www.oxfordjournals.org/nar/database/c/ Biological Database List | Nucleic Acid Research] | |
| − | : | + | :2012 NAR Database Summary Paper Category List |
| − | + | *[http://unite.ut.ee/ UNITE] | |
| + | :[http://www2.dpes.gu.se/project/unite/UNITE_intro.htm User-friendly Nordic ITS Ectomycorrhiza Database] | ||
| − | + | =Classificação e taxonomia= | |
| − | + | ||
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| − | == | + | ==Aplicativos Online== |
| + | *[http://eztaxon-e.ezbiocloud.net/images/taxon/eztaxon-e_bi.png Ez-Taxon] | ||
| + | :A prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species | ||
| − | + | ==Aplicativos Standalone== | |
| + | |||
| + | =Análises Metagenômicas= | ||
| + | |||
| + | *[http://orphelia.gobics.de/ Orphelia] | ||
| + | :Metagenomic ORF finder | ||
| + | |||
| + | *[http://exon.biology.gatech.edu/metagenome/Prediction/ MetaGene Mark] | ||
| + | :Gene Prediction in Metagenomes and Novel Prokaryotes by Heuristic Approach | ||
| + | |||
| + | *[http://www.sabiametagenome.lncc.br/login Sabia Metagenome] | ||
| + | :LNCC Sabia Metagenomic tool | ||
| + | |||
| + | *[http://www.labinfo.lncc.br/ LabInfo LNCC] | ||
| + | :Bioinformatics Lab (Labinfo) of the National Laboratory of Scientific Computation of the Ministry of Science and Technology (MCT) of Brazil | ||
| + | |||
| + | *[http://armbrustlab.ocean.washington.edu/seastar SEAStAR | Armbrust Lab] | ||
| + | :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". | ||
| + | |||
| + | *[http://www.cbcb.umd.edu/software/glimmer-mg/ Glimmer-MG :: Center for Bioinformatics and Computational Biology] | ||
| + | :Glimmer-MG is a system for finding genes in environmental shotgun DNA sequences. | ||
| + | |||
| + | *[http://ab.inf.uni-tuebingen.de/software/megan/ MEGAN] | ||
:MEtaGenome ANalyzer | :MEtaGenome ANalyzer | ||
| − | + | ||
| + | *[http://ab.inf.uni-tuebingen.de/software/megan/ JCVI Metarep] | ||
:Análises metagenômicas (necessita de sequencias anotadas) | :Análises metagenômicas (necessita de sequencias anotadas) | ||
| − | + | ||
| + | *[http://manatee.sourceforge.net/ JCVI Manatee] | ||
:Software de anotação de sequências | :Software de anotação de sequências | ||
| − | + | ||
| + | *[http://www.jcvi.org/cms/research/projects/annotation-service/ JCVI Annotation service] | ||
:Serviço de anotação de sequências | :Serviço de anotação de sequências | ||
| − | + | ||
| + | *[http://www.jcoast.net/ JCoast] | ||
: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. | :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. | ||
| − | + | ||
| + | *[http://www.cebitec.uni-bielefeld.de/groups/brf/software/gendb_info/index.html GenDB] | ||
:GenDB is a genome annotation system for prokaryotic genomes. | :GenDB is a genome annotation system for prokaryotic genomes. | ||
| − | + | ||
| + | *[http://metagenomics.anl.gov/ MG-RAST] | ||
:The Metagenomics RAST (online) | :The Metagenomics RAST (online) | ||
| − | + | ||
| + | *[http://www.megx.net/portal/content/content.html MegX] | ||
:Portal for marine ecological genomics | :Portal for marine ecological genomics | ||
| − | + | ||
| + | *[http://www.jgi.doe.gov/programs/GEBA/index.html JGI GEBA] | ||
:The GEBA project is aimed at systematically filling in the gaps in sequencing along the bacterial and archaeal branches of the tree of life. | :The GEBA project is aimed at systematically filling in the gaps in sequencing along the bacterial and archaeal branches of the tree of life. | ||
| − | + | ||
| + | *[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi IMG GEBA] | ||
:Integrated Microbial Genomes | :Integrated Microbial Genomes | ||
| − | + | ||
| + | *[http://nbc.ece.drexel.edu/index.php NBC] | ||
:Naïve Bayesian Classification tool | :Naïve Bayesian Classification tool | ||
| − | + | ||
| + | *[http://webcarma.cebitec.uni-bielefeld.de/cgi-bin/webcarma.cgi WebCarma] ([http://webcarma.cebitec.uni-bielefeld.de/cgi-bin/webcarma.cgi?PAGE=uploadData&NEW=1&SESSIONKEY=c0a3ccf4700e2e40e7bd47f7ee30b1194ab674296657c2481066384c630eefac&EMAIL=leonardonormando@gmail.com login]) | ||
:WebCARMA is a web-based system for the functional and taxonomic analysis of metagenomic DNA sequences. | :WebCARMA is a web-based system for the functional and taxonomic analysis of metagenomic DNA sequences. | ||
| − | + | ||
| + | *[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001061 PhyolOTU] | ||
:A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data | :A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data | ||
| − | + | ||
| + | *[https://portal.camera.calit2.net/gridsphere/gridsphere?cid=home CAMERA 2.0] | ||
:Community Cyberinfrastructure for Advanced Microbial Ecology Research & Analysis | :Community Cyberinfrastructure for Advanced Microbial Ecology Research & Analysis | ||
| − | + | ||
| + | *[https://img.jgi.doe.gov/cgi-bin/mer/main.cgi IMG MER] | ||
:IMG Metagenomics | :IMG Metagenomics | ||
| − | + | ||
| + | *[http://greengenes.lbl.gov/cgi-bin/nph-index.cgi GreenGenes] | ||
:The greengenes web application provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. | :The greengenes web application provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. | ||
| − | + | ||
| + | *[http://metaphyler.cbcb.umd.edu/ MetaPhyller] | ||
:Estimating Bacterial Composition from Metagenomic Sequences (linux) | :Estimating Bacterial Composition from Metagenomic Sequences (linux) | ||
| − | + | ||
| + | *[http://weizhong-lab.ucsd.edu/metagenomic-analysis/ WebMGA] | ||
:Ótimo framework com várias ferramentas online, como ORF_finder e fragGeneScan | :Ótimo framework com várias ferramentas online, como ORF_finder e fragGeneScan | ||
| − | + | ||
| + | *[http://omics.informatics.indiana.edu/FragGeneScan/ FragGeneScan] | ||
:Orf finder tool | :Orf finder tool | ||
| − | + | ||
| + | *[http://bioinformatics.oxfordjournals.org/content/26/6/715.full STAMP] | ||
:Statistical Analysis of Metagenomic Profile | :Statistical Analysis of Metagenomic Profile | ||
| + | *[http://metagenomics.atc.tcs.com/SPHINX/ SPHINX] | ||
| + | :An algorithm for taxonomic binning of metagenomic sequences [http://bioinformatics.oxfordjournals.org/content/early/2010/10/28/bioinformatics.btq608.full.pdf Artigo] | ||
| + | *[http://metagenomics.atc.tcs.com/binning/DiScRIBinATE/ DiScRIBinATE] | ||
| + | :DiScRIBinATE is a similarity based binning method. | ||
| + | *[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6033151&tag=1 Parallel-META] | ||
| + | :A high-performance computational pipeline for metagenomic data analysis | ||
| − | + | *[http://metastats.cbcb.umd.edu/detection.html MetaStats] | |
| − | : | + | :Metastats: Detect Differentially Abundant Features |
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| − | + | ||
| + | =Análises Estatísticas= | ||
| + | *[http://www.gromacs.org/ Gromacs] | ||
| + | :GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. | ||
| + | |||
| + | *[http://www.r-project.org/ R] | ||
| + | :The R Project for Statistical Computing | ||
| + | |||
| + | *[http://rstudio.org/ RStudio] | ||
| + | :RStudio™ is a new integrated development environment (IDE) for R. | ||
| + | |||
| + | =Plataformas de Desenvolvimento= | ||
| + | *[http://www.bioperl.org/wiki/Main_Page Bioperl] | ||
| + | :BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. | ||
| + | |||
| + | *[http://www.bioperl.org/wiki/Bioperl_scripts Bioperl Scripts] | ||
| + | :Scripts em BioPerl | ||
| + | |||
| + | *[http://nebc.nerc.ac.uk/tools/code-corner/scripts/scripts Bioinformatics Scripts NERC Institute] | ||
| + | : NERC Scripts for Bioinformatics | ||
| + | |||
| + | *[http://learnpythonthehardway.org/book/ Learn Python the hard way] | ||
| + | :Learn Python The Hard Way, 2nd Edition | ||
| + | |||
| + | *[http://www.programmingforbiologists.org/lectures-intro Lectures - Intro] | ||
| + | :Programming For Biologists | ||
| + | |||
| + | *[http://www.python.org/ Python] | ||
| + | **[http://numpy.scipy.org/ Numpy] | ||
| + | **[http://www.scipy.org/ Scipy] | ||
| + | *[http://www.perl.org/ Perl] | ||
| + | *[http://www.ruby-lang.org/en/ Ruby] | ||
| + | **[http://bioruby.org/ Bioruby] | ||
| + | *[http://www.java.com/en/ Java] | ||
| + | |||
| + | |||
| + | =Blogs e Tutoriais= | ||
| + | *[http://intro-prog-bioinfo-2010.wikispaces.com/ Python Bioinformatics Course] | ||
| + | :QB3 Python Bioinformatics Course 2010 | ||
| + | |||
| + | *[http://www.ncbi.nlm.nih.gov/feed/rss.cgi NCBI News] | ||
:NCBI RSS feed | :NCBI RSS feed | ||
| − | + | *[http://hot-bioinformatics.blogspot.com/ What’s hot in Bioinformatics] | |
:A personal blog about interesting news on the field of Bioinformatics, computational biology and related stuff | :A personal blog about interesting news on the field of Bioinformatics, computational biology and related stuff | ||
| − | + | ||
| − | + | *[http://bioinformatictools.blogspot.com/ Bionformatics Tools] | |
| + | |||
| + | *[http://biostar.stackexchange.com/questions/112/your-favorite-bioinformatics-blogs Lista de blogs] | ||
:Blogs de bioinformática | :Blogs de bioinformática | ||
| − | + | ||
| − | + | *[http://bcbio.wordpress.com/ Blue Collar bioinformatics] | |
| + | |||
| + | *[http://blog.mckuhn.de/ BioCS] | ||
:biology as computational science | :biology as computational science | ||
| − | + | ||
| + | *[http://finchtalk.geospiza.com/ Finch Talk] | ||
:Follow the conversation to learn how you can make the most of your data | :Follow the conversation to learn how you can make the most of your data | ||
| − | + | ||
| + | *[http://news.open-bio.org/news/ OBF] | ||
:Open source bioinfomatics | :Open source bioinfomatics | ||
| − | [http://www.mailund.dk/ Mailund] | + | |
| + | *[http://www.mailund.dk/ Mailund] | ||
:Computer science, bioinformatics, genetics, and everything in between | :Computer science, bioinformatics, genetics, and everything in between | ||
| − | + | ||
| + | *[http://learnr.wordpress.com/ Learning R] | ||
:As the title says, tips to learn R | :As the title says, tips to learn R | ||
| − | + | ||
| + | *[http://www.helixsoft.nl/blog/ Helix Soft] | ||
:Do mesmos desenvolvedores do [http://www.wikipathways.org/ wikiPathways] | :Do mesmos desenvolvedores do [http://www.wikipathways.org/ wikiPathways] | ||
| − | + | ||
| − | + | *[http://nsaunders.wordpress.com/ N Saunders] | |
| + | |||
| + | *[http://www.scivee.tv/ SciVee] | ||
:Science Youtube | :Science Youtube | ||
| − | + | ||
| − | + | *[http://www.bioinformaticszen.com/ Bioinformatics Zen] | |
| − | + | ||
| − | + | *Aprendendo R | |
| − | + | ||
| − | + | *[http://www.ats.ucla.edu/stat/r/ Learn R] | |
| − | + | ||
| − | + | *[http://leg.ufpr.br/Rpira/Rpira/ Curso R] | |
| + | |||
| + | *[http://www.quintiliano.prof.ufu.br/index_arquivos/EBR.pdf Introdução à estatística básica com R] | ||
| + | |||
| + | *[http://cran.r-project.org/doc/contrib/Krijnen-IntroBioInfStatistics.pdf Applied statistics for bioinformatics using R] | ||
| + | |||
| + | *[http://sourceforge.net/projects/tinn-r/ TINN-R] | ||
| + | |||
| + | *[http://www.sciviews.org/SciViews-R/ SciViews] | ||
:GUI for R | :GUI for R | ||
| − | + | ||
| + | *[http://www.bioconductor.org/ Bioconductor] | ||
:Diversos pacotes de análise Bioinformatica | :Diversos pacotes de análise Bioinformatica | ||
| − | + | ||
| − | Blog of Jonathan A. Eisen, evolutionary biologist, microbiologist and genomics researcher, | + | *[http://phylogenomics.blogspot.com/ Phylogenomics] |
| − | + | :Blog of Jonathan A. Eisen, evolutionary biologist, microbiologist and genomics researcher, | |
| − | + | ||
| + | *[http://thirdreviewer.com/ Third Reviewer] | ||
| + | |||
| + | *[http://clovr.org/category/blog/ CloVR] | ||
:Automated Sequence Analysis from Your Desktop | :Automated Sequence Analysis from Your Desktop | ||
| − | == | + | =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 | + | :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 atual tal como 14h39min de 4 de dezembro de 2012
Tabela de conteúdo |
[editar] Análise de sequências
- A high-quality package of free, Open Source software for molecular biology
- G-language Genome Analysis Environment provides a greater variety of useful genome analysis tools compared to most existing analysis software packages, and is also easily pluggable.
[editar] Estrutura de Proteínas
- Cn3D macromolecular structure viewer
- NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
[editar] Aplicativos Online
[editar] Aplicativos Standalone
- CodonCode Aligner is an easy-to-use program for sequence assembly, contig editing, and mutation detection.
[editar] Alinhamento de sequências
[editar] 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
[editar] 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.
[editar] Contig Assembly
[editar] 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
[editar] Classificação e taxonomia
[editar] Aplicativos Online
- A prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species
[editar] Aplicativos Standalone
[editar] 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
[editar] Análises Estatísticas
- GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
- The R Project for Statistical Computing
- RStudio™ is a new integrated development environment (IDE) for R.
[editar] 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
[editar] 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
- Aprendendo 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
[editar] 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
[editar] Idaho University - IBEST Applications (home brew!)
- MiCA Microbial Community Analysis
- HiTSA High Throughput Sequence Analysis
- Statgen Genetic Distances Statistical Generator
[editar] Phylogenetic Congruence
[editar] Phylogenetic Inference
- FastDNAml
- Garli
- GeneTree
- Mesquite
- ModelTest
- MrBayes
- P4
- PAML
- PAUP
- Seq-Gen
- Phylip
- Phyml
- RAxML
- RAxML web
- TreeView
- BEAST
