Lista de Ferramentas de Bioinformática
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==Aplicativos online e standalone== | ==Aplicativos online e standalone== | ||
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*[http://www.bioperl.org/wiki/Bioperl_scripts Bioperl Scripts] | *[http://www.bioperl.org/wiki/Bioperl_scripts Bioperl Scripts] | ||
:Scripts em BioPerl | :Scripts em BioPerl | ||
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| + | *[http://blip.codeplex.com/ BL!P: BLAST in Pivot] | ||
| + | *[http://www.ab.wur.nl/Cyrille2 Cyrille2 - Cyrille2 Wiki] | ||
| + | *[http://armbrustlab.ocean.washington.edu/seastar SEAStAR | Armbrust Lab] | ||
| + | *[http://www.programmingforbiologists.org/lectures-intro Lectures - Intro | Programming For Biologists] | ||
| + | *[http://www.cbcb.umd.edu/software/glimmer-mg/ Glimmer-MG :: Center for Bioinformatics and Computational Biology] | ||
| + | *[http://nebc.nerc.ac.uk/tools/code-corner/scripts/scripts Bioinformatics Scripts NERC Institute] | ||
| + | *[http://learnpythonthehardway.org/book/ Learn Python the hard way] | ||
| + | *[http://ged.msu.edu/angus/index.html Angus 2.0] | ||
| + | *[http://www.oxfordjournals.org/nar/database/c/ Biological Database List | Nucleic Acid Research] | ||
Edição de 11h21min de 26 de abril de 2012
Tabela de conteúdo |
Aplicativos online e standalone
- 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
- Wiki com uma lista de banco de dados biológicos
- QB3 Python Bioinformatics Course 2010
- GMOD is the Generic Model Organism Database project, a collection of open source software tools for creating and managing genome-scale biological databases
- Ferramentas on-line de alinhamento e criação de árvores
- Interative Tree of Life
- Compara réplicas de T-RFLP
- The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis.
- A prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species
- Metagenomic ORF finder
- Gene Prediction in Metagenomes and Novel Prokaryotes by Heuristic Approach
- Artemis is a free genome browser and annotation tool that allows visualisation of sequence features
- 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.
- Teste de modelos de alinhamento
- 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.
- LNCC Sabia Metagenomic tool
- Bioinformatics Lab (Labinfo) of the National Laboratory of Scientific Computation of the Ministry of Science and Technology (MCT) of Brazil
- Database for Annotation, Visualization and Integrated Discovery (DAVID )
- Scripts em BioPerl
- BL!P: BLAST in Pivot
- Cyrille2 - Cyrille2 Wiki
- SEAStAR | Armbrust Lab
- Lectures - Intro | Programming For Biologists
- Glimmer-MG :: Center for Bioinformatics and Computational Biology
- Bioinformatics Scripts NERC Institute
- Learn Python the hard way
- Angus 2.0
- Biological Database List | Nucleic Acid Research
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
- Metastats: Detect Differentially Abundant Features
- Lista de Ferramentas
- Bioinformatics Software
Platforms
Cluster Tools
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
