标签云

Alignment Allele-specific transcription Alternative Splicing Barcoding Bisulfite Sequencing Cancer biology ChIP-exo ChIP-on-chip ChIP-Seq Clone verification Comparative genomics Comparative transcriptomics Comparison Conversion Copy number estimation De novo assembly De novo sequencing De-novo assembly DNA methylation DNA-Seq Epigenomics Evaluation and validation Exome and whole genome variant detection Framework Functional Genomics Gene expression Gene regulatory network analysis General bioinformatics (pipeline) Genomic Assembly Genomic Assembly Evaluation Genomic Assembly Validation Genomics Identification InDel discovery Infrastructure Mapping Mass Accuracy Metagenomics Metatranscriptomics Next Generation Sequencing Nucleic acid sequence analysis Nucleic acid structure comparison Pairwise structure alignment Peptide identification (DB) Peptide identification (De novo) Peptide identification (lib match) Personal genomics Phylogenetics Population genetics Population Genomics Protein Inference Quality Control Quantitation Raw Data Raw Data / Conversion Read alignment Reference assembly Regulatory genomics Regulatory genomics epigenomics Resequencing Results processing RNA structure prediction RNA-Seq RNA-Seq Alignment RNA-Seq Quantitation Search and retrieval Sequence analysis Sequence database search Sequence functional annotation Sequence motif discovery Sequence motif recognition Sequence Quality Control Sequencing Small RNA transcriptome SNP Annotation SNP discovery SNPs Somatic mutations Structural variation Targeted assembly Targeted resequencing Transcription Factor Binding Site identification Transcriptome Viral genomics Whole gene prediction Whole Genome Resequencing Whole Genome Resequencing Analysis  Alignment  Alternative Splicing  Bisulfite Sequencing  ChIP-on-chip  ChIP-Seq  De novo assembly  De novo transcriptome assembly  De-novo assembly  DNA methylation  DNA-Seq  Exome and Whole genome variant detection  Fusion finding  Fusion genes  Fusion transcripts  Genomic Assembly  Genomics  Genotyping  High-throughput sequencing  In vitro selection  InDel discovery  Mapping  Metagenomics  MiRNA  MiRNA-Seq  Motif analysis  Next Generation Sequencing  Personal genomics  Phylogenetics  Population genetics  Population genomics  Read alignment  Reference assembly  Regulatory genomics  RNA Seq analysis  RNA-Seq  RNA-Seq Quantitation  Sequence analysis  Sequence annotation  Sequencing  Small RNA transcriptome  SNP discovery  Structural variation  Targeted resequencing  Transcription Factor Binding Site identification  Transcriptomics  Whole Genome Resequencing  Whole Genome Resequencing Analysis 基因组注释 基因预测 多重序列比对 多重比对 序列拼接 推荐 比较基因组 重复序列
1. MG-RAST
MG-RAST is a fully-automated service for annotating metagenome samples providing analysis tools for comparison
标签:Metagenomics, Phylogenetics,Metabolic reconstruction
2. PyroNoise
Clustering of pyrosequencing (454) data with noise model (AmpliconNoise) and chimaera removal (Perseus) for sequence diversity analysis.
标签:Phylogenetics, Metagenomics
3. ERGO Genome Analysis and Discovery System
ERGO provides a systems-biology informatics toolkit centered on comparative genomics to capture, query and visualize sequenced genomes. Building upon the most comprehensive genomic database available anywhere integrated with the largest collection of microbial metabolic and non-metaboli...
标签:Metabolic reconstruction,Phylogenetics, Comparative genomics, SNP Annotation, SNP discovery, Alignment, Exome analysis, Metagenomics,Pathway analysis, Comparative transcriptomics, Functional Genomics, Gene Expression Analysis, Genome Wide Association Stud
4. Biopython
Biopython provides a tool kit for writing bioinformatics and computational molecular biology software in Python.
标签:Sequence analysis,Phylogenetics, Population genetics, Protein structures
5. Blixem
a graphical blast viewer
标签:Sequence analysis,Phylogenetics, Homology
6. SeqAn
C++ template library with many sequence analysis algorithms and datastructures.
标签:Sequence analysis, Genomics,Phylogenetics
7. CANGS
CANGS is a flexible and user-friendly utility to trim sequences, filter low quality sequences, and produce input files for further downstream analyses for 454 sequences. CANGS can be used to assign the taxonomic grouping based on similarity with sequences from the NCBI database a u...
标签:Metagenomics, Phylogenetics
8. Lasergene
Lasergene is a comprehensive DNA and protein sequence analysis software suite comprised of seven applications which include functions ranging from sequence assembly and SNP detection, to automated virtual cloning and primer design.
标签:Alignment, De novo sequencing,De-novo assembly, Genomics,InDel discovery, Integrated solution, Mapping,Phylogenetics, Protein structure analysis, Read alignment, SNP discovery,Sequence analysis,Transcription Factor Binding Site identification
9. Metaxa
Metaxa uses Hidden Markov Models to identify, extract and classify small-subunit (SSU) rRNA sequences (12S/16S/18S) of bacterial, archaeal, eukaryotic, chloroplast and mitochondrial origin in metagenomes and other large sequence sets
标签:Metagenomics, Phylogenetics,Sequence analysis, Community analysis
10. Megraft
Megraft is a software tool to graft ribosomal small subunit (16S/18S) fragments from metagenomes onto full-length SSU sequences, enabling accurate diversity estimates from fragmentary and non-overlapping sequence data.
标签:Metagenomics, Phylogenetics,Sequence analysis, Community analysis, Rarefaction
11. Sequedex
Sequedex classifies short reads for phylogeny and function at high speed
标签:Metagenomics, Phylogenetics,Genomics
12. BBMap
BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.
标签:Resequencing, Alignment,Quality Control, RNA-Seq Alignment, Alternative Splicing, Whole Genome Resequencing, SNP discovery,Phylogenetics, Metagenomics,Read Binning
13. UGENE
UGENE is a free cross-platform genome analysis suite that combines popular bioinformatics tools within a single user friendly interface.
标签:Phylogenetics, Genomics,Sequence analysis, Protein structure analysis
14. Nesoni
Nesoni is a high-throughput sequencing data analysis toolset.
标签:RNA-Seq Alignment, SNP discovery, Phylogenetics
15. BioSmalltalk
BioSmalltalk provides an environment to build bioinformatics scripts and applications using the most powerful object technology as of today, the Smalltalk programming environment
标签:Sequence analysis,Phylogenetics, Population genetics, Protein structures
16. FaBox
Tools for splitting, joining and otherwise manipulating FASTA format sequence files.
标签:Phylogenetics, Genomic Assembly
17. Geneious
Search, organize and analyze genomic and protein information of any size via desktop program that provides publication ready images to enhance the impact of your research.
标签:Phylogenetics, Sequence analysis, De-novo assembly,Genomics, Population genetics,Metagenomics, Structural variation, RNA-Seq,Epigenomics
18. MrBayes
"MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters." Program for the Bayesian estimation of phylogeny.
标签:Phylogenetics
19. RAST
"RAST (Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating complete or nearly complete bacterial and archaeal genomes. It provides high quality genome annotations for these genomes across the whole phylogenetic tree."
标签:Genomics, Phylogenetics