Software

• Archive
  • IUBio Archive - an archive of biology data and software (Indiana Univ.)
  • BioCatalog - a software directory of general interest in molecular biology and genetics
  • CSSJ Software World - provides the original chemical softwares
  • Genome Net anonymous FTP server
  • NCBI anonymous FTP server
  • Software Available for NIH Research Community
• Alignment editor
  • GeneDoc - a full featured Multiple Sequence Format (.MSF) file alignment editor [Win]
  • SeaView - a graphical multiple sequence alignment editor. can handle MSF, CLUSTAL, FASTA, PHYLIP, MASE formats. [UNIX]
• Chemistry
  • Chime [FREE] [Win/Mac]
  • ISIS/Draw - Chemical structure presentation [FREE] [Win/Mac]
• Sequencing
  • ABIF Viewer 3100 [Win]
  • ABIView - ABIView displays the trace and basecall data of ABI automatic DNA sequencing files. [Win]
  • Chromas - a Windows application which displays and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files which the analysis programs for ALF and Li-Cor sequencers can create. [Win]
  • EditView for Macintosh - view and print analyzed sample files containing sequence data from an ABI PRISM 373, 377 or 310 Genetic Analyzer. [Mac]
  • Phred/Phrap/Consed - the most famous base-caller/assembler/contig editor
  • Phred/Phrap for Windows & MacOS
  • SPS Phrap - parallelized Phrap, faster than the original phrap even if with single CPU
• Imaging
  • NIH IMAGE
  • Scion Image for Windows - a porting of NIH Image to Windows
  • Oracio'n Medical Viewer - a medical viewer supports DICOM and Papyrus
• Phylogenetic study
  • NJplot - tree drawing program [Mac|Win|Unix]
  • Phylogenetic Analysis by Maximum Likelihood (PAML) - PowerMAC, Windows 95/NT and UNIX
  • PAUP
  • Phylip - a free package of programs for inferring phylogenies. Windows and Macintosh executables are available.
  • Phylogeny Programs Available Elsewhere
  • TreeView - Tree drawing software for Apple Macintosh and Windows
• Plasmid drawing
  • CloneMap & MacPlasmap
  • pDRAW32 - beerware
  • Plasmid ARTIST
  • Plasmid Maker [Mac]
  • PlasMapper - web-based plasmid drawing with auto-annotation [NAR vol. 32 (2004)]
  • Plasmid Processor - a simple tool for plasmid presentation
  • WinPlas
• BioPerl Project
• Dotter - a graphical dotplot program [Unix/Win]
• The EMBL Sander Group
• MTRisk - predicts functionally important domains of a protein from only a single cDNA sequence for the protein
• PubCrawler - a PubMed robot.
• W2H - a WWW Interface to the GCG Sequence Analysis Software Tools