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Phylum-for-free Amplify
v1.2 DNAid
v1.8 ClustalX MacPlasmap
v1.8.2 Primers!
v1.0 RasMac
v2.6 SeqView
v1.0.1 Speakquencer
v1.4 Swiss-PdbViewer
3.5 (Mac Version) Download
the user guide here
Note: to be able to consult the
help directly from within Swiss-PdbViewer, place the
content of this folder into the Swiss-PdbViewer
"_stuff_" folder.
Phylum is a Mac based image archiving
software product designed specifically for research and
education use. It supports non standard scientific formats
such as 16 bit grey scale and 48 bit color images in
addition to JPEG, TIFF and PICT files. The product has an
easy to use Mac interface and allows you to manage, organise
and present your images in galleries, movies and
hierarchical image libraries.The free version, which can be
downloaded here, is a fully functional application with a
limit of 5,000 images. Details on the product are available
at http://www.phylumforfree.com
. The product is completely free, however you will have to
register
in order to use it.
This software is for use in
designing, analyzing, and simulating experiments involving
the polymerase chain reaction (PCR). Given a template
sequence and two primers, it will predict the possible
outputs of the PCR, taking into account also weak matches to
the target sequence. Freeware, thanks to Bill
Engels
As the author says, "DNAid is not a
heavyweight package which will run your 'just-sequenced
gene' through every prediction or analysis algorithm in the
known universe." However, it is a very usefull application
that allows to perform all the basic manipulations of DNA
sequences such as restriction mapping, translation,
reverse-complement and others. Freeware, thanks to
Frédéric Dardel
Clustal X provides a new window-based
user interface to the popular Clustal W multiple alignment
program. Performs multiple alignments of DNA and protein
sequences right on your mac. Freely available to the
scientific comunity
It draws, stores, and prints
high-quality circular plasmid maps with the data you
specify. Fully functional. Shareware! Please read the
enclosed documents before using the application
Primers! is a very popular Macintosh
utility to aid scientists in picking precisely the PCR
oligos which fit their needs.Imput the target sequence and a
range of selection, and Primers! will sugest the best PCR
primers to amplify the selected region. Shareware at your
discretion, thanks to Richard J. Resnick (Apple
Pi Software). Please read
the "Read Me" file before using the application. Requires
any Macintosh with a Color monitor and System 7 or beyond. A
web version of the program can be accessed at
http://www.williamstone.com/primers/
It is straigthforward to use.
An advantage of the www version is that you always use the
most updated version of the software.
RasMac is the Mac version of RasMol, a
molecular graphics freeware program intended for the
visualisation of proteins, nucleic acids and small
molecules, written by Roger Sayle.You can downlod structural
coordinates for a molecule of your choice -FOR
INSTANCE HERE-
and view, rotate and customize
the look of the molecule right on your Mac even with no
structural biology background (Thank you Roger Sayle!).
Great for educational purposes. An excellent
web site maintained by Eric
Martz, for download and informations on RasMol
and CHIME,
a RasMol version designed as browser plug-in,
can
be found HERE. Before using
RasMac, please read the enclosed "Notice" file
SeqVu is an alignment editor with
analysis options that allows you to work quickly and simply
with multiple sequences. It is ideal for manually correcting
and obtaining publication-quality pictures from alignments
produced using alignment software such as ClustalV or GCG
pileup. Fully functional. Shareware.
Speakquencer is a tool for
entering and/or verifying nucleotide or amino acid sequence
information. The application reads pre-existing sequences or
speaks sequence as it is entered form the keyboard.
Freeware, thanks to Christian Fritze
Free Molecular visualization
software by Nicolas Guex and Manuel C. Peitsch.
Swiss-PdbViewer is an application that provides a user
friendly interface allowing to analyse 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. For
informations, tutorials, and to download the viewer for
other platforms (PC, SGI, Linux) visit the Swiss
PdbViewer official site at
expasy.
Download
DNA Strider and other Molecular Biology applications from the MB
Shortcuts software section
OTHER SITES FOR MAC SOFTWARE DOWNLOADMolecular Biology and Scietific Software Software for Molecular Biology (Sunet) Software for Molecular Biology (@Weizmann) Mac Scientific Software (A huge list! @mwn.net) Pure Mac Molecular biology software Art's Free Software Page (List of free software that is relevant to the Molecular Biology and Structural Biology fields. For different platforms: mac-windows-unix)
General Software
A couple of "PC-only" links to plasmids/genetic maps drawing applications AcaClone pDRAW32 Freeware DNA cloning, analysis and visualisation software (Only for PCs running Windows 95, 98, NT4 or NT2000 ) Redasoft The main product of Redasoft is "Plasmid", an application designed to help in the drawing of high quality vector maps and constructs and perform DNA sequence analysis quickly and easily. Plasmid includes unique and innovative features such as an integrated web browser and the ability to instantly convert sequence files from the Internet into fully labeled graphical maps! Have a tour. (for Windows 95 / 98 / NT / 2000) MORE SOFTWARE LINKSJava3D Molecular Visualisation System Is a continually developing freeware molecular visualisation tool implemented using Sun Microsystem's Java in addition to the new Java3D Application Programming Interface. JMVS is free and distributed with its Java/Java3D Source Code which may be used and modified as detailed in the source code headers. About.com Biology Software links Phylogeny software Some 168 phylogeny packages and 17 free servers. Infos and downloads RASA 2.3 Update Update page for RASA software for measuring phylogenetic signal, detecting long branches, and more. RasMol and Chime Molecular visualisation Software Download, tutorials and links Genamics.com/Software Genamics SoftwareSeek is a respository and database of freely-distributable and commercial tools for use in molecular biology and biochemistry. Windows, MS-DOS, Mac, Unix and Linux platforms are supported, as well as online tools that run through your internet browser. ARTICLE:
"Free
Software in Molecular Biology for Macintosh and MS Windows
computers"
By Don Gilbert, june 1998. The definitive resource. |