Tools

• boxshade • MSA pretty printer • [more]
  boxshade  •  Boxshade is a program for creating good looking printouts from multiple-aligned protein or DNA sequences.  [less]
• Codon Suite • codon-based sequence analysis • [more]
  Codon Suite  •  The CodonSuite server takes as input inframe coding DNA sequences and then performs various codon-based comparisons- codon-based alignments, a codon distance-based tree, SynPAM distance estimates and estimates of Nei and Gojoboris dN and dS.  [less]
• Dotlet • sequence similarity plots • [more]
  Dotlet  •  Diagonal plots to graphically compare of biological sequences and identify regions of close similarity [less]
• MADAP • clustering for genome annotation data • [more]
  MADAP  •  MADAP is a flexible clustering tool for the interpretation of one-dimensional genome annotation data. Such data might consist of counts, probabilities, or intensities associated with genome positions. They may be generated by mapping mRNA 5' and 3' sequence tags to genomes, by ChIP-chip or ChIP-Seq assays, or by genome-wide genotype-phenotype association studies. MADAP identifies clusters of data points corresponding to genomic features. [less]
• Newick Utilities • high-throughput phylogenetic tree processing • [more]
  Newick Utilities  •  The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. [less]
• Phylogibbs • regulatory sites discovery • [more]
  Phylogibbs  •  Phylogibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences,including multiple alignments of orthologous sequences from related organisms.The algorithm uses a Gibbs sampling strategy, takes the phylogenetic relationships of the input sequences rigorously into account, and assigns realistic posterior probabilities to reported sites using a novel annealing+tracking strategy. [less]
• SIBsim4 • expressed and genomic sequence alignment • [more]
  SIBsim4  •  SIBsim4 is a modified version of the sim4 program, which is a similarity-based tool for aligning an expressed DNA sequence (EST, mRNA) with a genomic sequence. [less]
• T-Coffee • sequence and structure multiple alignments • [more]
  T-Coffee  •  A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures [less]