Lista de Ferramentas de Bioinformática
De Lembiotech Wiki
Tabela de conteúdo |
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.
Estrutura de Proteínas
- Cn3D macromolecular structure viewer
- NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
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 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.
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
- 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
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
