Lista de Ferramentas de Bioinformática
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| + | *[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= | =Alinhamento de sequências= | ||
Edição de 11h52min de 26 de abril de 2012
ORGANIZAR EM UMA DAS CATEGORIAS ABAIXO
- 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 )
Análise de sequências
Aplicativos Online
Aplicativos Standalone
*CodonCode Aligner :CodonCode Aligner is an easy-to-use program for sequence assembly, contig editing, and mutation detection.
Alinhamento de sequências
==Aplicativos Online== *Blast NCBI Online :NCBI Basic Local Alignment Search Tool
*Embl Tools :Bioinformatics Tools for Sequence Similarity & Analysis Searching
*EsyPred3D :Predição de estruturas protéicas 3D
*Phylogeny.fr :Ferramentas on-line de alinhamento e criação de árvores
*iTol :Interative Tree of Life
*ModelTest :Teste de modelos de alinhamento
==Aplicativos Standalone== *Clustal :Multiple alignment of nucleic acid and protein sequences
*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.
==Bancos de Dados Biológicos== *List of biological databases :Wiki com uma lista de banco de dados biológicos
*ARB :The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis.
Classificação e taxonomia
==Aplicativos Online== *Ez-Taxon :A prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species
==Aplicativos Standalone==
Análises Metagenômica
- 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
Análises Estatísticas
Plataformas de Desenvolvimento
*Bioperl :BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl.
*Bioperl Scripts :Scripts em BioPerl
Blogs e Tutoriais
*Python Bioinformatics Course :QB3 Python Bioinformatics Course 2010
Aplicativos e ferramentas
- 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
Idaho University - 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 metagenômicas
- 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
- compares a nucleotide query sequence translated in all reading frames against a protein sequence database
- 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
Blogs e Tutoriais
- 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
Análises estatísticas
- The R Project for Statistical Computing
- RStudio™ is a new integrated development environment (IDE) for R.
