Introduces the partially ordered alignment algorithm and demonstrates how this graph based alignment visualization provides a more compact view of complex alignments. A novel method for multiple alignment of sequences with repeated and shuffled elements. Visualising biological data: a semantic approach to tool and database integration. TreeGraph: automated drawing of complex tree figures using an extensible tree description format.

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Treevolution: visual analysis of phylogenetic trees. TreeDyn: towards dynamic graphics and annotations for analyses of trees. Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling.

INTREPID–INformation-theoretic TREe traversal for Protein functional site IDentification. Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Visualising very large phylogenetic trees in three dimensional hyperbolic space. Visualizing large hierarchical clusters in hyperbolic space. Reconciliation with non-binary species trees. NOTUNG: a program for dating gene duplications and optimizing gene family trees. VISSA: a program to visualize structural features from structure sequence alignment. The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. JEvTrace: refinement and variations of the evolutionary trace in JAVA. Detecting species-site dependencies in large multiple sequence alignments. A method to predict functional residues in proteins. Correlated substitution analysis and the prediction of amino acid structural contacts. Ensemble approach to predict specificity determinants: benchmarking and validation. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. Zvelebil, M.J., Barton, G.J., Taylor, W.R. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes. Jalview Version 2–a multiple sequence alignment editor and analysis workbench. Waterhouse, A.M., Procter, J.B., Martin, D.M., Clamp, M. CINEMA-MX: a modular multiple alignment editor. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. To our knowledge, this is the first detailed analysis of the errors that may be introduced by tree based sequence alignment algorithms. Characterization of pairwise and multiple sequence alignment errors. MEME SUITE: tools for motif discovery and searching. HotSwap for bioinformatics: a STRAP tutorial. Integrated sequence analysis for the Macintosh. PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments. Twenty years of Delila and molecular information theory: the Altenberg-Austin Workshop in Theoretical Biology biological information, beyond metaphor: causality, explanation, and unification Altenberg, Austria, 11–14 July 2002. Sequence logos: a new way to display consensus sequences. Analysis and prediction of functionally important sites in proteins. The empirical analysis underlying the 'Taylor' amino acid color scheme this builds on Taylor's earlier work (1986) concerning approaches for the classification of amino acids. Amino acid encoding schemes from protein structure alignments: multi-dimensional vectors to describe residue types.

Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX. CHROMA: consensus-based colouring of multiple alignments for publication. ALSCRIPT: a tool to format multiple sequence alignments. ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy. Raghava, G.P., Searle, S.M., Audley, P.C., Barber, J.D. A comprehensive review of the approaches available for the alignment of many sequences. T-Coffee: A novel method for fast and accurate multiple sequence alignment. Multiple sequence alignment using ClustalW and ClustalX. Vector NTI, a balanced all-in-one sequence analysis suite. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.