Lista de Ferramentas de Bioinformática
(Diferença entre revisões)
(→Análises metagenômicas) |
|||
Linha 48: | Linha 48: | ||
:Scripts em BioPerl | :Scripts em BioPerl | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | === 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] | ||
+ | |||
+ | === Sequence Analysis === | ||
+ | |||
+ | * [http://emboss.sourceforge.net/ EMBOSS] | ||
+ | * [http://www.g-language.org/wiki/ G-Language] | ||
+ | |||
+ | === Sequence Alignment === | ||
+ | |||
+ | * [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] | ||
+ | |||
+ | === 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] | ||
+ | |||
+ | === Protein Structure === | ||
+ | |||
+ | * [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] | ||
+ | *[http://www.ks.uiuc.edu/Research/namd/ Namd] | ||
+ | * [http://www.umass.edu/microbio/rasmol/ Rasmol] | ||
+ | * [[Xplor]] | ||
+ | |||
+ | === Statistical/Mathematical Packages === | ||
+ | |||
+ | * [[Gromacs]] | ||
+ | * [http://www.r-project.org/ R] | ||
+ | |||
+ | === Contig Assembly === | ||
+ | |||
+ | * [http://www.phrap.org/phredphrapconsed.html Phred/Phrap/Consed] | ||
+ | * [http://www.repeatmasker.org/webrepeatmaskerhelp.html RepeatMasker] | ||
+ | * [http://seq.cs.iastate.edu/ Cap3] | ||
+ | |||
+ | ===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] | ||
+ | |||
+ | ==Platforms== | ||
+ | *[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] | ||
+ | |||
+ | ==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]] | ||
+ | |||
+ | ==January 2011 Module Crossover== | ||
+ | Workflow on homogenizing module applications on firefly and fourtytwo (and all archs of all clusters in the future): | ||
+ | |||
+ | change path to $apps: | ||
+ | set apps $env(MODULE_APP_PATH) | ||
==Análises de sequências e alinhamento== | ==Análises de sequências e alinhamento== | ||
Edição de 09h28min de 24 de novembro de 2011
Tabela de conteúdo |
Aplicativos online e standalone
- 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
- Integrated Microbial Genomes System
- The Integrated Microbial Genomes (IMG) is a genome browsing and annotation system
- List of biological databases
- Wiki com uma lista de banco de dados biológicos
- Python Bioinformatics Course
- QB3 Python Bioinformatics Course 2010
- GMOD
- GMOD is the Generic Model Organism Database project, a collection of open source software tools for creating and managing genome-scale biological databases
- Phylogeny.fr
- Ferramentas on-line de alinhamento e criação de árvores
- iTol
- Interative Tree of Life
- t-Align
- Compara réplicas de T-RFLP
- ARB
- The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis.
- Orphelia
- Metagenomic ORF finder
- MetaGene Mark
- Gene Prediction in Metagenomes and Novel Prokaryotes by Heuristic Approach
- Artemis
- Artemis is a free genome browser and annotation tool that allows visualisation of sequence features
- 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.
- ModelTest
- Teste de modelos de alinhamento
- 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.
- Sabia Metagenome
- LNCC Sabia Metagenomic tool
- LabInfo LNCC
- Bioinformatics Lab (Labinfo) of the National Laboratory of Scientific Computation of the Ministry of Science and Technology (MCT) of Brazil
- David
- Database for Annotation, Visualization and Integrated Discovery (DAVID )
- Bioperl Scripts
- Scripts em BioPerl
IBEST Applications - home brew!
- MiCA Microbial Community Analysis
- HiTSA High Throughput Sequence Analysis
- Statgen Genetic Distances Statistical Generator
Sequence Analysis
Sequence Alignment
Phylogenetic Congruence
Phylogenetic Inference
- FastDNAml
- Garli
- GeneTree
- Mesquite
- ModelTest
- MrBayes
- P4
- PAML
- PAUP
- Seq-Gen
- Phylip
- Phyml
- RAxML
- RAxML web
- TreeView
- BEAST
Population Genetics
Protein Structure
Statistical/Mathematical Packages
Contig Assembly
Misc
Platforms
Cluster Tools
January 2011 Module Crossover
Workflow on homogenizing module applications on firefly and fourtytwo (and all archs of all clusters in the future):
change path to $apps:
set apps $env(MODULE_APP_PATH)
Análises de sequências e alinhamento
- Embl Tools
- Bioinformatics Tools for Sequence Similarity & Analysis Searching
- NCBI Tools
- EsyPred3D
- Predição de estruturas protéicas 3D
- Bioperl
- BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl.
- Blast NCBI Online
- NCBI Basic Local Alignment Search Tool
- CodonCode Aligner
- CodonCode Aligner is an easy-to-use program for sequence assembly, contig editing, and mutation detection.
- Clustal
- Multiple alignment of nucleic acid and protein sequences
Análises metagenômicas
- MEGAN
- MEtaGenome ANalyzer
- JCVI Metarep
- Análises metagenômicas (necessita de sequencias anotadas)
- JCVI Manatee
- Software de anotação de sequências
- JCVI Annotation service
- Serviço de anotação de sequências
- 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.
- GenDB
- GenDB is a genome annotation system for prokaryotic genomes.
- MG-RAST
- The Metagenomics RAST (online)
- MegX
- Portal for marine ecological genomics
- 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.
- IMG GEBA
- Integrated Microbial Genomes
- NBC
- Naïve Bayesian Classification tool
- WebCarma (login)
- WebCARMA is a web-based system for the functional and taxonomic analysis of metagenomic DNA sequences.
- PhyolOTU
- A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data
- CAMERA 2.0
- Community Cyberinfrastructure for Advanced Microbial Ecology Research & Analysis
- IMG MER
- IMG Metagenomics
- GreenGenes
- The greengenes web application provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading.
- MetaPhyller
- Estimating Bacterial Composition from Metagenomic Sequences (linux)
- WebMGA
- Ótimo framework com várias ferramentas online, como ORF_finder e fragGeneScan
- FragGeneScan
- Orf finder tool
- STAMP
- Statistical Analysis of Metagenomic Profile
- MultiBlastX
- compares a nucleotide query sequence translated in all reading frames against a protein sequence database
- SPHINX
- An algorithm for taxonomic binning of metagenomic sequences Artigo
- DiScRIBinATE
- DiScRIBinATE is a similarity based binning method.
- Parallel-META
- A high-performance computational pipeline for metagenomic data analysis
Blogs e Tutoriais
- NCBI News
- NCBI RSS feed
- What’s hot in Bioinformatics
- A personal blog about interesting news on the field of Bioinformatics, computational biology and related stuff
- Bionformatics Tools
- Lista de blogs
- Blogs de bioinformática
- Blue Collar bioinformatics
- BioCS
- biology as computational science
- Finch Talk
- Follow the conversation to learn how you can make the most of your data
- OBF
- Open source bioinfomatics
- Computer science, bioinformatics, genetics, and everything in between
- Learning R
- As the title says, tips to learn R
- Helix Soft
- Do mesmos desenvolvedores do wikiPathways
- N Saunders
- SciVee
- Science Youtube
- Bioinformatics Zen
- Aprendendo R
- Learn R
- Curso R
- Introdução à estatística básica com R
- Applied statistics for bioinformatics using R
- TINN-R
- SciViews
- GUI for R
- Bioconductor
- Diversos pacotes de análise Bioinformatica
- Phylogenomics
Blog of Jonathan A. Eisen, evolutionary biologist, microbiologist and genomics researcher,
- Third Reviewer
- CloVR
- Automated Sequence Analysis from Your Desktop