Collection of protein and alignment tools

 

• AlineAline is an interactive perl/tk application which can read common sequence alignment formats which the user can then alter, embellish, markup etc to produce the kind of sequence figure commonly found in biochemical articles.
• AnnHyb AnnHyb is a tool for working with and managing nucleotide sequences in multiple formats. The features includes format conversion, sequence viewer, sequence editor, oligonucleotides alignment, restriction analysis, pattern searching, retrieval from servers, multi-alignment viewer, consensus determination ...
• ANTHEPROT (ANalyse THE PROTeins) is the result of about 10 years of biocomputing activity of a group of the Institute of Biology and Chemistry of Proteins.
• Base-By-BaseBase-By-Base is a whole genome pairwise and multiple alignment editor.
• ModView, visualization of multiple protein sequences and structures.
• AlScript Alscript is a program to format
  multiple sequence alignments in PostScript
• AMAS This server allows you to run AMAS on your own multiple sequence alignment. If you would like to run AMAS on your own Unix computer, you can obtain the package
• AMPS BALLView is our stand-alone molecular modeling and visualization application. Furthermore it is also a framework for developing molecular visualization functionality. It is available free of charge for Linux, Windows and MacOS.
• AMPS AMPS is a suite of programs designed for the multiple alignment of protein sequences and flexible pattern matching. This computer package implements a heuristic approach to multiple sequence alignment that has been shown to be effective for many protein families
• BelVu Belvu is an X-windows viewer for multiple sequence alignments. One of the main advantages of Belvu is that it has an extensive set of modes to color the residues. There are several ways to color them by conservation and by residue type (user-configurable). Other useful features are fetching of the Swissprot (or PIR) entries by double clicking and easy tracking of the position in the alignment.
• BioEdit BioEditis a biological sequence alignment editor written for Windows 95/98/NT/2000/XP.; An intuitive multiple document interface with convenient features; makes alignment and manipulation; of sequences relatively easy on your desktop computer. Several sequence manipulation and analysis options and links to external anaylsis programs facilitate a working environment which allows you to view and manipulate sequences with simple point-and-click operations.
• CLS Gene WorkbenchCLC Gene Workbench creates a software environment enabling users to make a large number of advanced DNA sequence analyses, combined with smooth data management, and excellent graphical viewing and output options.
• BoxShade BOXSHADE : printouts from multiple-aligned protein or DNA sequences (Hofmann, Baron)
• Chimera UCSF Chimera is a highly extensible, interactive molecular graphics program. It is the successor to UCSF Midas and MidasPlus
• Cinema MX Cinema is a platform independent excellent alignment editor written in Java
• CHROMA CHROMA

  CHROMA is a tool for generating annotated multiple sequence alignments in a convenient format for publication
  

• DCSE: Dedicated Comparative Sequence Editor
• Dinamo DINAMO: interactive protein alignment and model building.
  Bentz J, Baucom A, Hansen M, Gregoret L.
• Dnaplot
• ICM-Browser ICM-Browser provides a biologist or a chemist with direct access to the treasures of structural biology and protein families. It reads PDB files or alignment files directly from the database web-sites and provides rich professional molecular graphics environment with powerful representations of proteins, DNA and RNA, and multiple sequence alignments.
• JaMBW Given a sequence and the features which are annotated in its sequence, this program produces a visual display which allows to tightly interact with features, sequence and access at the full text of the specified feature.
• Jevtrace evtrace is a implementation of the Evolutionary Trace (ET) method. The software expands on the ET and allows manipulation of input data and parameters. A number of novel tree inspired analysis of protein families are available. Jevtrace consists of a graphical frontend and backend for data manipulation and algorithm infrastructure.
• Joy joy is an analysis and formatting program for multiple protein sequence alignments or single protein structures. It was developed to display three-dimensional (3D) structural information in a sequence alignment and help to understand the conservation of amino acids in their specific local environments.
• ESPript ESPript, Easy Sequencing in Postscript, is a utility to generate a pretty PostScript output from aligned sequences.
• GeneDoc

  A Full Featured Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows.

  • Data Analysis and Visualization.
  • Score assisted manual alignment.
  • Paginated Printouts.
  • Windows Based.
  • Highly Configurable.
  • Exported Figures.
  • Phylogenetic Tree support.
• GeneiousResearch software for biologists, not computer scientists.
• Indonesia Indonesia is an integrated program package for biological sequence analysis. The program is written in Java2 and a graphical user interface is an integrated part of the program.
• JavaShade: JavaShade is an interactive drawing program for preparing previously-generated multiple sequence alignments for publication, and for looking at the conservation of residues across the alignment.
• InteralignINTERALIGN is a dedicated user friendly alignment editor including a view of secondary structures and a synchronized display of quality carbon alpha traces of corresponding protein structures.
• Jalview Jalview is a tool written in Java to analyse the residue conservation patterns in a protein multiple alignment as well as being an interactive alignment editor.
• LalnView LalnView is a graphical program for visualizing local alignments between two sequences (protein or nucleic acids). Sequences are represented by colored rectangles to give an overall picture of the similarities between the two sequences. Blocks of similarity between the two sequences are colored according to the degree of identity between segments.
• MACAW: Alignments were generated interactively using the Multiple Alignment Construction and Analysis Workbench (MACAW) computer application
• MAFFT+XCED MAFFT is an multiple alignment program for amino acid or nucleotide sequences
  XCED is a graphical front-end for MAFFT
• MEGA The objective of the MEGA2 software is to provide tools for exploring, discovering, and analyzing DNA and protein sequences from evolutionary perspectives.
• MOE MOE possesses a powerful and flexible facility for multiple sequence and multiple structure alignment of protein chains. A unique feature of MOEs protein alignment tool, MOE-Align, is that it allows mixed structural and non-structured data.
• MPSA MPSA is a software intented to the protein sequence analysis. It provides many methods and tools integrated in a graphical user interface available on several operating systems.
• MSD Welcome to the EBI Macromolecular Structure Database - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB).
• PFAAT Pfaat is a Java-based protein sequence alignment application designed to facilitate the analysis, curation, and annotation of large protein sequence families.
• SAM Sequence Alignment and Modeling System
• Se-Al Se-Al is an application for creating multiple sequence alignments from nucleotide and amino acid sequences. At the moment it does not do any automatic alignments but is intended for the production of hand alignments and for preparing input for alignment programs such as CLUSTAL and phylogeny reconstruction programs such as PHYLIP and PAUP.
• SeaView SeaView is a graphical multiple sequence alignment editor developped by Manolo Gouy. SeaView is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE).
• seq-mode: "I seem to end up doing manual editing with the one true editor to fix up protein sequence and alignment files every time, no matter how automatic the tools I am using are supposed to be."
• Swiss-PdbViewer Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
• SeqApp SeqApp is a freeware Macintosh program written by Don Gilbert and available by anonymous ftp (Fetch) or gopher from ftp.bio.indiana.edu. SeqApp is a powerful program- it is used for storing and aligning data, and outputting formatted files for PHYLIP, PAUP, and other analysis programs as well as for printing hard copies of alignments.
• SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools SinicView
• T-Coffee: T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures.
• UgeneThe ultimate goal of the project is to integrate popular bioinformatics tools and algorithms within a single visual interface that can be easily used by molecular biologists
• VissaVISSA, (VIsualize Structure Sequence Alignment) is a program that can visualize both multiple sequence alignment and 3D structure and can also map residues from alignment onto 3D structure and vice versa.
• Vito ViTO is a tool that is useful for:
  • optimizing the alignment of a sequence onto one or several template structure. Historically this was the first use of ViTO and what initiated the project.
  • checking structural alignments.
  • studying a protein family: it helps to identify where clusters of conserved residues in a protein family fall in 3D space.
  • mapping sequence variations within a protein family in 3D space. (i.e. dynamic evolutionnary trace).
• Vista VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species (VISTA browser).