Online Bioinformatics Tools v2

Daniel Ocampo Daza, PhD student
Department of Neuroscience
Uppsala Universitet
Box 593
SE-75124 Uppsala, Sweden

daniel.ocampo-daza[at]neuro.uu.se
Tel: +46-(0)18-471 44 05

This is the space where I collect the diverse online bioinformatics resources and tools that I find useful. They're mostly within the field of vertebrate genomics and phylogenetics. I will keep updating continuously as I find new cool stuff to add to the list.
If you want to suggest a resource that's missing from this page, leave me a comment at this page.

www.egosumdaniel.se

Genome databases

Ensembl Genome Browser: assembled and annotated vertebrate genomes
EnsemblGenomes: invertebrate, protist, plant, fungi and bacterial genomes
Pre!Ensembl: draft assemblies of vertebrate genomes
JGI Genome Portal: large collection of genome ref. sequences, some assembled
NCBI Genomic Map Viewer: search and browse reference sequences for a large collection of genomes
NCBI Genomic Trace Archive
UCSC Genome Bioinformatics: ref. sequences and draft assemblies of various genomes
HGSC Genome Data: includes invertebrate genomes not available on other browsers
Spotted gar genome sequence: assembled linkage groups at NCBI Genome database
Elephant Shark Genome Project
Vertebrate TimeCapsule: Transcriptome database - bichir, hagfish and cloudy dogfish ESTs
Oikopleura Genome Browser
SpBase: Purple sea urchin genome database
StellaBase: Sea anemone genome database
Silkworm Genome Database
BeeBase: Honey bee genomic resources

Evolutionary resources

TimeTree :: The Timescale of Life: Extensive resource that allows you to search for divergence times between taxa - includes updated sources from the scientific literature as well as book chapters
Tree of Life Web Project: Less focus on phylogeny and divergence times, but with summarized info pages on the different taxa

Reference databases

Entrez cross-database search: Mine NCBI's reference sequence databases
HMMER web server: Mine reference sequence and protein domain databases using profile hidden Markov model algorithms.
GeneCards: Human gene database incl. nomenclature and genomic info
Gene Characterization Index
IUPHAR Database: Receptor and ion channel nomenclature and classification
InterPro: Protein sequence analysis and domain classification
TreeFam: Gene family/orthology/paralogy database
OPTIC: Orthology prediction database

Synteny databases

Genomicus: integrated synteny genome browser
SyntenyDB: offers several graphical comparisons of Ensembl genome data
Cinteny: fast identification of syntenic chromosome blocks
Chromhome: Chromosome homology mapping (mammals)

Sequence manipulation and alignment web tools

The Sequence Manipulation Suite: Direct translation or show translation in all reading frames, ORF finder, reverse complement et c
ClustalW Multiple Sequence Alignment: Online execution of the ClustalW alignment algorithm
Sequence and phylogeny data format converter: Convert files between Newick, Nexus, Phylip, Clustal and Fasta formats.
BEAUti: Convert Nexus files into XML

Sequence analysis and alignment software

ClustalX: The most quick & useful sequence alignment and phylogenetic (NJ, UPGMA) tree application
MAFFT: Sequence alignment and phylogenetic (NJ, UPGMA) software, both download and online execution
CLC Sequence Viewer: Very versatile and complete sequence manipulation, alignment (multiple methods) and phylogenetic tree (NJ, UPGMA) application.
JalView: Sequence analysis and alignment application incorporating the JABAWS 2 package of multiple sequence alignment tools as well as some phylogenetic tree functions
eBioX: Very versatile and easy to use sequence analysis and alignment tool for Mac
Se-Al: Simple sequence analysis and alignment application (doesn't run on Mac OS X 10.7)
BioEdit (Win only): Versatile, if a bit complex, sequence analysis application with a greater variety of functions

Phylogeny software

MolecularEvolution.org: Includes updated links to a selection of commonly used bioinformatic software for molecular evolution, including PAML, PAUP*, PHYLIP and others
Felsenstein lab - Phylogeny Programs: A huge selection of most, if not all, commonly used phylogeny software
The Phylogenetic Handbook Software: Another extensive selection of phylogeny software
MEGA 4 (Win/Linux only): Phylogenetic tree software (NJ, MP)
TreePuzzle: Phylogenetic tree software (QPML)
PhyML 3.0: Phylogenetic Maximum Likelihood algorithm application, both web-based and executable
BEAST: Bayesian analysis of molecular sequences/phylogenies
MrBayes: Bayesian inference of molecular phylogenies
Phycas: Bayesian inference of phylogeny from nucleotide sequences
RAxML BlackBox: Online execution of the Randomized Axelerated Maximum Likelihood program
Garli Web Service v2.0: Online execution of Genetic Algorithm for Rapid Likelihood Inference/download version
ProtTest: Calculates the best amino acid substitution model for phylogenetic analyses jModelTest: Calculates the best nucleotide substitution model for phylogenetic analyses

Phylogenetic tree viewers and editors

FigTree: The best phylogenetic tree viewer
TreeView X and TreeView (older version): Phylogenetic tree viewer
TreeThief: Manual phylogenetic tree entry
TreeSnatcher Plus: Phylogenetic tree capturing

Prediction Tools

PSIPRED Server: Protein structure prediciton server - includes other prediction methods than just PSIPRED
CBS Prediction Servers: Includes the very useful TMHMM transmembrane domain prediction and SignalP (signal peptide) prediction, among others
GenScan Web Server: Predict gene structures from genomic sequence
TMPro: Transmembrane helix prediction
PFam: Protein family and domain structure database with sequence-based search function
InterProScan: Sequence-based search against the InterPro protein domain database
ADDA: Automatic Domain Decomposition Algorithm with several search functions
JPred 3: Secondary strcuture prediction server
SplicePort: Splice site analysis and prediction tool
Phobius: Combined transmembrane topology and signal peptide predictor
PredictProtein: Protein prediction tool incorporating secondary structure, transmembrane helices, binding sites et c

Other useful applications and tools

TextWrangler (Mac only): Great general purpose text editor, transformer and manipulator - supports most alignment and phylogenetic tree formats
Notepad++: Versatile source-code and notepad application for Windows
PROSITE My Domains: Create and draw protein domain images
WebLogo: Create sequence logo images of conserved sequence motifs

Tutorials/Guides

Ensembl tutorials: Guides to the Ensembl genome browser and its features
CLCbio Bioinformatics Explained: Basic bioinformatics background theory
Phylogenetic tree formats: Small tutorial on the commonly used Newick and Nexus formats.