03-327/727 Bioinformatics Resources

This year, we will use

• Jalview to calculate and visualize multiple sequence alignments,
• Topali for selecting an appropriate model of sequence evolution, and
• Seaview for evolutionary tree reconstruction

Multipurpose Phylogenetic Software Packages

• Jalview
  • Multiple sequence alignment visualization and editor.
  • Can launch several multiple alignment algorithms to run removely on servers at the University of Dundee.
  • Runs as an applet or locally on your machine.
  • Downloadable software, all platforms (I think), source code.
  • Jalview tutorial Screencast
  • Jalview reference card
• Seaview
  • Runs on Windows (all OS versions), MAC OS 10, Linux, Sun Solaris.
  • ''...a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.''
• TOPALi
  • "Statistical and evolutionary analysis of multiple sequence alignments"
  • Provides a graphical user interface to Model Generator, and supports analyses on codon usage, recombination, and signatures of selection. Can also be used to construct trees using ML and Bayesian methods. TOPALi takes a multiple alignment as input. It will not align sequences for you.
  • Runs on Windows, MAC OS 10, Linux, Sun Solaris.
• Mega
  • Runs on Windows (all OS versions), MAC OS 10, Linux.
  • "... 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."

Multiple Sequence Alignment

• Bioinformatics Tools for Multiple Sequence Alignment/EBI
  • Web service with access to a suite of MSA programs, including Clustal Omega, ClustalW2, DbClustal, Kalign, MAFFT, MUSCLE, MView, T-Coffee.
• MUSCLE
  • Downloadable software; Unix, MAC OS, Windows.
• MAFFT
  • Downloadable software; Unix, MAC OS, Windows.
• CLUSTAL
  • Downloadable software; Unix, MAC OS, Windows XP, source code.
• ProbCons
  • Web server, downloadable source code (C++).

Tree visualization tools

• Figtree

Online Taxonomic resources

• NCBI common tree
  • This web site takes a list of species names as input and generates a species tree, which can be downloaded in newick format. It is very conservative and is likely to produce species trees with many polytomies.
•   NCBI's list of taxonomy resources
  • This is a list of taxonomic resources outside of NCBI, including both general information about species names and classification and links to resources for specific species lineages (e.g., algae, fungi, ...).
• Species identification codes
  • This gives a complete list of the five letter taxonomic codes used by uniprot. Each code is indexed to the latin binomial and common name of the species.
• Tree of Life web project
  • This is a species tree in hypertext format. The goal is to have one page for each taxon with links to immediate ancestors and dscendants. Individual pages are curated by domain experts. It has beautiful images and is excellent in areas where the pages are well curated. Unfortunately, some lineages are not well curated. It is very useful for the base of the vertebrates, but not particularly useful for mammals, for example.
• PATRIC  Pathosystems Resource Integration Center
  • A broad spectrum of information about bacteria, especially pathogenic bacteria, including phylogenies.
• JGI Genome Portal 
  • The DOE-funded Joint Genomes Institute's informatic resource. They primarily sequence microbes. The informatic resource provides access to a variety of types of informationa about these these genomes include phylogenetic information and blast searches.
• MistDB 2.1 
  • This is a primarily a resource for signal transduction systems in bacteria, but the taxonomy browser is a useful way to find sequenced genomes.
• TimeTree
  • The Time Scale of Life: Species trees with divergence time estimates.
• UC Berkeley Museum of Paleonology Online Exhibits
  •   UCMP Taxon Lift

Multiple Alignment Editors

• GeneDoc
  • Windows only; source code. Despite the references to outdated Windows versions, this will run on Windows 7.
  • GeneDoc documentation Login in as "guest", click MODULES, then GENEDOC. This site also includes a GeneDoc tutorial video. Unfortunately, the "help" function in the GeneDoc GUI does not work.

Motif based sequence analysis tools

• MEME web service.

General Resources

• National Center for Biotechnology Information (NCBI)
  • Information and tutorials at NCBI
  
  
• Uniprot, a protein knowledgebase.
  • Species identification codes
  
  
• YGOB, Yeast Genome Order Browser.


• GOLD - Genomes Online Database


• Felsenstein's list of phylogeny programs


• Pittsburgh Supercomputing Center Biomedical Initiative
  
  • Sequence Analysis Resources
  
  
  • PSC Online Tutorials