Data viewing and editing tools
- Artemis: A DNA Sequence Viewer and Annotation Tool
- BioNJ
- Circos
- FigTree - Graphical viewer of phylogenetic trees
- GhostScript
- GNUPlot
- IGV - Integrative Genomics Viewer - high-performance visualization tool for interactive exploration of genomic datasets
- iTOL - Interactive Tree Of Life
- Krona - Hierarchical data browser
- Tablet - Lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments
DNA assembly tools
DNA progressive assembly
- GenSeed - A seed-driven progressive assembly program
- GenSeed-HMM - Progressive assembly tool using DNA, protein or profile HMMs as seeds
Gene prediction tools
Linux - distributions and interfaces
Metabolic pathways - databases
Metagenomics - tools and web servers
- JGI IMG - Integrated Microbial Genomes and Metagenomes
- MEGAN6 - MEtaGenome ANalyzer
- MetaPhlAn v2.0 - Metagenomic Phylogenetic Analysis
- MetaPhyler - Estimating Bacterial Composition from Metagenomic Sequences
- MetaVelvet - de novo metagenomic assembler
- MG-RAST - web-based platform for data intensive biomedical research
- PhyloPythia - Accurate phylogenetic classification of variable-length DNA fragments
- QIIME - Quantitative Insights Into Microbial Ecology
Molecular phylogeny
Multiple sequence alignment
Ontologies
Orthology - databases
- COG - Clusters of Orthologous Groups
- eggNOG
- KO - KEGG Orthology
- InParanoid
- OrthoMCL DB
- pVOGs - prokaryotic Virus Orthologous Groups pVOGs
- vFam - HMMER3 database of profile HMMs built from viral proteins of RefSeq
Pipelines and workflows - plataforms
- Galaxy - web-based platform for data intensive biomedical research
- MAKER - portable and easily configurable genome annotation pipeline
- EGene - pipeline generation system for sequence processing and annotation
Proteins - databases of families, domains and motifs
- CATH - classification of protein structures downloaded from the Protein Data Bank
- CDD - Conserved Domains Database
- eMOTIF - database of highly specific and sensitive protein sequence motifs
- InterPro - protein sequence analysis & classification
- Pfam - database of protein families, each represented by multiple sequence alignments and HMMs
- PIR - Protein Information Resource
- PRINTS - compendium of protein fingerprints
- ProDom - collection of protein domain families automatically generated from the UniProt Knowledge Database
- PROSITE - Database of protein domains, families and functional sites
- SCOP - Structural Classification of Proteins
- SMART - Simple Modular Architecture Research Tool
- TIGRFAMs - TIGR Protein Families
- UniProtKB/Swiss-Prot - manually annotated and reviewed section of the UniProtKB
Protein motif search
Scientific journals on Bioinformatics / Virology
Sequence alignment and mapping - Tools
Sequence analysis packages
Sequence and annotation data formats
Sequence data trimming and processing
- Cutadapt - Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence
- FASTX-Toolkit - Command line tools for Short-Reads FASTA/FASTQ files preprocessing
- Samtools - Tools for manipulating next-generation sequencing data
- TrimAL - Automated removal of spurious sequences or poorly aligned regions
- Trim Galore - Wrapper script to automate quality and adapter trimming as well as quality control
- Trimmomatic - A flexible read trimming tool for Illumina NGS data
Sequence databases
- NCBI - National Center for Biotechnology Information
- DDBJ - DNA Data Bank of Japan
- EBI - European Bioinformatics Institute
- Uniprot
Similarity search
Tutorials
Virtualization - programs for virtual machine construction
- Parallels - virtual machines for Mac (commercial)
- VirtualBox - virtual machines for Win, Mac and Linux (freeware)
- WMWare - virtual machines for Win, Mac andLinux (commercial and freeware)
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