SearchIO, Download

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Matching the names in BioPerl, Biopython has a [[SeqIO]] module for sequence file input/output, and [[AlignIO]] for multiple sequence alignment input/output. The third member of the BioPerl trio is SearchIO, and a Biopython equivalent is being worked on in summer 2012 by [[Google Summer of Code]] student Wibowo Arindrarto ([http://bow.web.id/blog/tag/gsoc/ blog]).
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= Current Release - 1.60 - 25 June 2012 =
  
The final module name in Biopython isn't settled, but Bio.SearchIO is being used initially. This will cover pairwise sequence search file input/output, for example from BLAST, HMMER or Bill Pearson's FASTA suite. See the [http://www.bioperl.org/wiki/HOWTO:SearchIO BioPerl SearchIO HOWTO] for background.
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See also [https://github.com/biopython/biopython/raw/master/NEWS What's new].
  
This is expected to be included in Biopython 1.61 as an ''experimental'' module, and is already available from our source code repository if you want to test it.
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=== Files ===
 +
 
 +
* [http://biopython.org/DIST/biopython-1.60.tar.gz biopython-1.60.tar.gz] 9,280 Kb -- Source Tarball
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* [http://biopython.org/DIST/biopython-1.60.zip biopython-1.60.zip] 10,051 Kb -- Source Zip File
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* [http://biopython.org/DIST/biopython-1.60.win32-py2.5.exe biopython-1.60.win32-py2.5.exe] 1,469 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.60.win32-py2.6.exe biopython-1.60.win32-py2.6.exe] 1,492 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
 +
* [http://biopython.org/DIST/biopython-1.60.win32-py2.7.exe biopython-1.60.win32-py2.7.exe] 1,1618 Kb -- 32 bit Windows Installer for Python 2.7 and NumPy 1.5
 +
* [http://biopython.org/DIST/biopython-1.60.win32-py3.2-beta.exe biopython-1.60.win32-py3.2-beta.exe] 1,611 Kb -- 32 bit Windows Installer for Python 3.2 and NumPy 1.5 (''beta'' status for testing)
 +
 
 +
Please report any issues on our [[mailing lists]] or [http://redmine.open-bio.org/projects/biopython bug tracker].
 +
 
 +
Note we don't (yet) have official 64 bit Windows Installers - however, Christoph Gohlke has
 +
kindly made [http://www.lfd.uci.edu/~gohlke/pythonlibs/ Windows 64bit installers] for
 +
NumPy and Biopython (and other tools) available for testing.
 +
 
 +
=== Installation Instructions ===
 +
 
 +
For Windows we provide click-and-run installers (specific to your version of python), but you will first need to install some prerequisite software (listed below, in particular, NumPy).
 +
 
 +
Most Linux distributions will include an optional Biopython package (described below), and will take care of any prerequisite software automatically.
 +
 
 +
For Mac OS X, we recommend installing from source (see below). Under (Snow) Leopard, you will need to have installed Apple's XCode tools ''including'' the optional 10.4 SDK (check the option for 10.4 support when installing Xcode tools) which comes on DVD with the computer. For Lion, just install XCode from the Apple App Store (it is a big download).
 +
 
 +
Otherwise you typically install from source by downloading and uncompressing the archive, then running the commands:
 +
 
 +
python setup.py build
 +
python setup.py test
 +
sudo python setup.py install
 +
 
 +
If you have trouble, see the full installation instructions:
 +
 
 +
* [http://biopython.org/DIST/docs/install/Installation.html HTML Full Installation Instructions]
 +
* [http://biopython.org/DIST/docs/install/Installation.pdf PDF Full Installation Instructions]
 +
 
 +
If you are still stuck, sign up to the [[Mailing_lists|Biopython mailing list]] and ask for help there.
 +
 
 +
=== Required Software ===
 +
 
 +
* [http://www.python.org Python 2.5, 2.6 or 2.7] (Biopython 1.56 was the last release to officially support Python 2.4, although Biopython 1.58 should work)
 +
* [http://www.python.org/doc/current/inst/inst.html C compiler (if compiling from source)] You need a C compiler supported by distutils, gcc will work fine on UNIX-like platforms.  This is not needed on Windows if using the install programs provided above. On Mac OS, we recommend you install Apple's XCode ''including'' the 10.4 SDK if offered.
 +
* [http://numpy.scipy.org/ NumPy (Numerical Python)]. Note that until Biopython 1.49, Biopython used the older Numeric library.  We have tested NumPy 1.1 to 1.5 with Biopython.
 +
 
 +
=== Optional Software ===
 +
 
 +
For compiling Biopython:
 +
* [http://flex.sourceforge.net/ flex: The Fast Lexical Analyzer] -- for building Bio.PDB.mmCIF.MMCIFlex which is used to parse macromolecular Crystallographic Information Files (mmCIF)
 +
 
 +
Some parts of Biopython use the following additional python libraries:
 +
* [http://www.reportlab.org/downloads.html ReportLab] -- used for pdf graphics code
 +
* [http://sourceforge.net/projects/mysql-python MySQLdb] -- used for [[BioSQL]] with a MySQL database
 +
 
 +
In addition Biopython includes wrapper code for calling a number of third party command line tools including:
 +
* [http://www.ebi.ac.uk/Wise2/ Wise2] -- for command line tool dnal
 +
* [http://www.ncbi.nlm.nih.gov/blast/download.shtml NCBI Standalone BLAST] -- command line tool for running BLAST on your local machine
 +
* [ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/ Clustalw] -- command line tool for building sequence alignments
 +
* [http://cmpg.unibe.ch/software/simcoal2/ SIMCOAL2] and [http://www.rubic.rdg.ac.uk/~mab/software.html FDist] -- command line tools for population genetics
 +
* [http://emboss.sourceforge.net/ EMBOSS] -- lots of useful command line tools.
 +
 
 +
= Easy Install =
 +
 
 +
We don't officially sanction this option, but it has been reported to work fine.
 +
If you have [http://peak.telecommunity.com/DevCenter/EasyInstall easy_install] installed on your computer, you can download and install the latest Biopython distribution by simply executing this command:
 +
 
 +
<pre>
 +
easy_install -f http://biopython.org/DIST/ biopython
 +
</pre>
 +
 
 +
You will have to have administrator's rights to do this. On a Unix style system this is normally done by:
 +
 
 +
<pre>
 +
sudo easy_install -f http://biopython.org/DIST/ biopython
 +
</pre>
 +
 
 +
= Packages =
 +
 
 +
For those of you using Linux, the easiest way to install Biopython is through your distribution's package management system.  However, unless you are running a recent release of your Linux Distribution, you may find that the Biopython packages available to be a little out of date.  You might want to see if there is a backport available, otherwise you will have to install Biopython from source.
 +
 
 +
=== Ubuntu or Debian ===
 +
 
 +
You should be able to install Biopython and its dependencies using the Synaptic GUI tool (on the main menu under System / Administration / Synaptic Package Manager), or at the command line using:
 +
 
 +
sudo apt-get install python-biopython
 +
 
 +
If you want the documentation and unit tests,
 +
 
 +
sudo apt-get install python-biopython-doc
 +
 
 +
And if you want to use [[BioSQL]],
 +
 
 +
sudo apt-get install python-biopython-sql
 +
 
 +
However, this will probably not be the latest release (see [http://packages.ubuntu.com/python-biopython Ubuntu listing here], and [http://packages.debian.org/search?searchon=sourcenames&keywords=biopython Debian listing here]).  If you want the latest version of Biopython, you will need to install it from source.  However, you should be able to automatically install the build dependencies with the following command:
 +
 
 +
sudo apt-get build-dep python-biopython
 +
 
 +
Note: You may need to additionally install the NumPy package by hand, as a very out of date repository may still expect Biopython to use Numeric instead.
 +
 
 +
=== Fedora ===
 +
 
 +
Biopython is an official Fedora package (since Fedora 5).  The package is named [https://admin.fedoraproject.org/community/?package=python-biopython#package_maintenance python-biopython], and can be installed using yum as root:
 +
 
 +
yum install python-biopython
 +
 
 +
or via one of the GUI package management systems such as pirut and PackageKit (available in F-9 and later).
 +
 
 +
=== Gentoo Linux ===
 +
 
 +
Gentoo's portage tree contains an ebuild (sci-biology/biopython) which builds from source.  To install it, open a terminal as root and run:
 +
 
 +
emerge -va biopython
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 +
[http://www.gentoo-portage.com/sci-biology/biopython Here] is a link to Biopython at [http://www.gentoo-portage.com Gentoo-Portage] which shows the latest versions in Gentoo's Portage tree.
 +
 
 +
= Ports =
 +
 
 +
===FreeBSD===
 +
 
 +
The most easy way of installing Biopython in [http://www.freebsd.org/ FreeBSD] is through the [http://www.freebsd.org/ports/ Ports Collection]. If you're new to this procedure please take a look at [http://www.freebsd.org/doc/en_US.ISO8859-1/books/handbook/ports-using.html this document]. Supposing that you're familiar with this method and that you have an up-to-date ports tree, all you need to do is to execute the following commands as root:
 +
 
 +
<bash>
 +
cd /usr/ports/biology/py-biopython
 +
make install clean
 +
</bash>
 +
 
 +
Due to the great architecture of the ports system, this simple commands will automatically fetch and install Biopython (as well as its necessary dependencies).
 +
 
 +
= Old Releases =
 +
 
 +
Recent releases of Biopython require NumPy (and not Numeric):
 +
 
 +
* [http://biopython.org/DIST/biopython-1.59.tar.gz biopython-1.59.tar.gz] 8,377 Kb -- Source Tarball (24 February 2012)
 +
* [http://biopython.org/DIST/biopython-1.59.zip biopython-1.59.zip] 9,127 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.59.win32-py2.5.exe biopython-1.59.win32-py2.5.exe] 1,440 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.59.win32-py2.6.exe biopython-1.59.win32-py2.6.exe] 1,463 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
 +
* [http://biopython.org/DIST/biopython-1.59.win32-py2.7.exe biopython-1.59.win32-py2.7.exe] 1,590 Kb -- 32 bit Windows Installer for Python 2.7 and NumPy 1.5
 +
 
 +
* [http://biopython.org/DIST/biopython-1.58.tar.gz biopython-1.58.tar.gz] 7,847 Kb -- Source Tarball (18 August 2011)
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* [http://biopython.org/DIST/biopython-1.58.zip biopython-1.58.zip] 8,474 Kb -- Source Zip File
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* [http://biopython.org/DIST/biopython-1.58.win32-py2.4-unsupported.exe biopython-1.58.win32-py2.4-unsupported.exe] 1,427 Kb -- 32 bit Windows Installer for Python 2.4 (which we no longer officially support) and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.58.win32-py2.5.exe biopython-1.58.win32-py2.5.exe] 1,428 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.58.win32-py2.6.exe biopython-1.58.win32-py2.6.exe] 1,450 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
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* [http://biopython.org/DIST/biopython-1.58.win32-py2.7.exe biopython-1.58.win32-py2.7.exe] 1,577 Kb -- 32 bit Windows Installer for Python 2.7 and NumPy 1.5
 +
 
 +
* [http://biopython.org/DIST/biopython-1.57.tar.gz biopython-1.57.tar.gz] 6,783 Kb -- Source Tarball (2 April 2011)
 +
* [http://biopython.org/DIST/biopython-1.57.zip biopython-1.57.zip] 7,446 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.57.win32-py2.4-unsupported.exe biopython-1.57.win32-py2.4-unsupported.exe] 1,405 Kb -- 32 bit Windows Installer for Python 2.4 (which we no longer officially support) and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.57.win32-py2.5.exe biopython-1.57.win32-py2.5.exe] 1,405 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.57.win32-py2.6.exe biopython-1.57.win32-py2.6.exe] 1,428 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
 +
* [http://biopython.org/DIST/biopython-1.57.win32-py2.7.exe biopython-1.57.win32-py2.7.exe] 1,555 Kb -- 32 bit Windows Installer for Python 2.7 and NumPy 1.5
 +
 
 +
* [http://biopython.org/DIST/biopython-1.56.tar.gz biopython-1.56.tar.gz] 6,778 Kb -- Source Tarball (26 November 2010)
 +
* [http://biopython.org/DIST/biopython-1.56.zip biopython-1.56.zip] 7,347 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.56.win32-py2.4.exe biopython-1.56.win32-py2.4.exe] 1,429 Kb -- 32 bit Windows Installer for Python 2.4 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.56.win32-py2.5.exe biopython-1.56.win32-py2.5.exe] 1,429 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.56.win32-py2.6.exe biopython-1.56.win32-py2.6.exe] 1,451 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
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* [http://biopython.org/DIST/biopython-1.56.win32-py2.7.exe biopython-1.56.win32-py2.7.exe] 1,578 Kb -- 32 bit Windows Installer for Python 2.7 and NumPy 1.5
 +
 
 +
* [http://biopython.org/DIST/biopython-1.55.tar.gz biopython-1.55.tar.gz] 6,493 Kb -- Source Tarball (31 August 2010)
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* [http://biopython.org/DIST/biopython-1.55.zip biopython-1.55.zip] 7,058 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.55.win32-py2.4.exe biopython-1.55.win32-py2.4.exe] 1,448 Kb -- 32 bit Windows Installer for Python 2.4 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.55.win32-py2.5.exe biopython-1.55.win32-py2.5.exe] 1,449 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.55.win32-py2.6.exe biopython-1.55.win32-py2.6.exe] 1,471 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
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* [http://biopython.org/DIST/biopython-1.55.win32-py2.7.exe biopython-1.55.win32-py2.7.exe] 1,598 Kb -- 32 bit Windows Installer for Python 2.7 and NumPy 1.5
 +
 
 +
* [http://biopython.org/DIST/biopython-1.55b.tar.gz biopython-1.55b.tar.gz] 6,428 Kb -- Source Tarball (August 18, 2010)
 +
* [http://biopython.org/DIST/biopython-1.55b.zip biopython-1.55b.zip] 6,996 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.55b.win32-py2.4.exe biopython-1.55b.win32-py2.4.exe] 1,451 Kb -- 32 bit Windows Installer for Python 2.4 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.55b.win32-py2.5.exe biopython-1.55b.win32-py2.5.exe] 1,451 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.55b.win32-py2.6.exe biopython-1.55b.win32-py2.6.exe] 1,474 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
 +
 
 +
* [http://biopython.org/DIST/biopython-1.54.tar.gz biopython-1.54.tar.gz] 6,295 Kb -- Source Tarball (May 20, 2010)
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* [http://biopython.org/DIST/biopython-1.54.zip biopython-1.54.zip] 6,859 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.54.win32-py2.4.exe biopython-1.54.win32-py2.4.exe] 1,434 Kb -- 32 bit Windows Installer for Python 2.4 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.54.win32-py2.5.exe biopython-1.54.win32-py2.5.exe] 1,434 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.54.win32-py2.6.exe biopython-1.54.win32-py2.6.exe] 1,457 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
 +
 
 +
* [http://biopython.org/DIST/biopython-1.54b.tar.gz biopython-1.54b.tar.gz] 6,554 Kb -- Source Tarball (April 2, 2010)
 +
* [http://biopython.org/DIST/biopython-1.54b.zip biopython-1.54b.zip] 7,118 Kb -- Source Zip File
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* [http://biopython.org/DIST/biopython-1.54b.win32-py2.4.exe biopython-1.54b.win32-py2.4.exe] 1,426 Kb -- 32 bit Windows Installer for Python 2.4 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.54b.win32-py2.5.exe biopython-1.54b.win32-py2.5.exe] 1,427 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.54b.win32-py2.6.exe biopython-1.54b.win32-py2.6.exe] 1,456 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
 +
 
 +
* [http://biopython.org/DIST/biopython-1.53.tar.gz biopython-1.53.tar.gz] 4,185 Kb -- Source Tarball (December 15, 2009)
 +
* [http://biopython.org/DIST/biopython-1.53.zip biopython-1.53.zip] 4,652 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.53.win32-py2.4.exe biopython-1.53.win32-py2.4.exe] 1,129 Kb -- 32 bit Windows Installer for Python 2.4 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.53.win32-py2.5.exe biopython-1.53.win32-py2.5.exe] 1,130 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.53.win32-py2.6.exe biopython-1.53.win32-py2.6.exe] 1,155 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
 +
 
 +
* [http://biopython.org/DIST/biopython-1.52.tar.gz biopython-1.52.tar.gz] 5,486 Kb -- Source Tarball (September 22, 2009)
 +
* [http://biopython.org/DIST/biopython-1.52.zip biopython-1.52.zip] 5,930 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.52.win32-py2.4.exe biopython-1.52.win32-py2.4.exe] 1,107 Kb -- 32 bit Windows Installer for Python 2.4 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.52.win32-py2.5.exe biopython-1.52.win32-py2.5.exe] 1,108 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.52.win32-py2.6.exe biopython-1.52.win32-py2.6.exe] 1,147 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
 +
 
 +
* [http://biopython.org/DIST/biopython-1.51.tar.gz biopython-1.51.tar.gz] 5,428 Kb -- Source Tarball (August 17, 2009)
 +
* [http://biopython.org/DIST/biopython-1.51.zip biopython-1.51.zip] 5,922 Kb -- Source Zip File
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* [http://biopython.org/DIST/biopython-1.51.win32-py2.4.exe biopython-1.51.win32-py2.4.exe] 1,166 Kb -- Windows Installer for Python 2.4 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.51.win32-py2.5.exe biopython-1.51.win32-py2.5.exe] 1,167 Kb -- Windows Installer for Python 2.5 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.51.win32-py2.6.exe biopython-1.51.win32-py2.6.exe] 1,206 Kb -- Windows Installer for Python 2.6 and NumPy 1.3
 +
 
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* [http://biopython.org/DIST/biopython-1.51b.tar.gz biopython-1.51b.tar.gz] 5,172 Kb -- Source Tarball (June 23, 2009)
 +
* [http://biopython.org/DIST/biopython-1.51b.zip biopython-1.51b.zip] 5,605 Kb -- Source Zip File
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* [http://biopython.org/DIST/biopython-1.51b.win32-py2.4.exe biopython-1.51b.win32-py2.4.exe] 1,161 Kb -- Windows Installer for Python 2.4 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.51b.win32-py2.5.exe biopython-1.51b.win32-py2.5.exe] 1,161 Kb -- Windows Installer for Python 2.5 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.51b.win32-py2.6.exe biopython-1.51b.win32-py2.6.exe] 1,199 Kb -- Windows Installer for Python 2.6 and NumPy 1.3
 +
 
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* [http://biopython.org/DIST/biopython-1.50.tar.gz biopython-1.50.tar.gz] 4,550 Kb -- Source Tarball (April 20, 2009)
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* [http://biopython.org/DIST/biopython-1.50.zip biopython-1.50.zip] 4,988 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.50.win32-py2.3.exe biopython-1.50.win32-py2.3.exe] 1,228 Kb -- Windows Installer for Python 2.3 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.50.win32-py2.4.exe biopython-1.50.win32-py2.4.exe] 1,232 Kb -- Windows Installer for Python 2.4 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.50.win32-py2.5.exe biopython-1.50.win32-py2.5.exe] 1,232 Kb -- Windows Installer for Python 2.5 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.50.win32-py2.6.exe biopython-1.50.win32-py2.6.exe] 1,270 Kb -- Windows Installer for Python 2.6 and NumPy 1.3
 +
 
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* [http://biopython.org/DIST/biopython-1.50b.tar.gz biopython-1.50b.tar.gz] 4,788 Kb (April 3, 2009)
 +
* [http://biopython.org/DIST/biopython-1.50b.zip biopython-1.50b.zip] 5,250 Kb
 +
* [http://biopython.org/DIST/biopython-1.50b.win32-py2.3.exe biopython-1.50b.win32-py2.3.exe] 1,226 Kb -- Windows Installer for Python 2.3 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.50b.win32-py2.4.exe biopython-1.50b.win32-py2.4.exe] 1,230 Kb -- Windows Installer for Python 2.4 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.50b.win32-py2.5.exe biopython-1.50b.win32-py2.5.exe] 1,230 Kb -- Windows Installer for Python 2.5 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.50b.win32-py2.6.exe biopython-1.50b.win32-py2.6.exe] 1,268 Kb -- Windows Installer for Python 2.6 and NumPy 1.3
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* [http://biopython.org/DIST/biopython-1.49.tar.gz biopython-1.49.tar.gz] 4,052 Kb (November 21, 2008)
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* [http://biopython.org/DIST/biopython-1.49.zip biopython-1.49.zip] 4,498 Kb
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* [http://biopython.org/DIST/biopython-1.49.win32-py2.3.exe biopython-1.49.win32-py2.3.exe] 1,111 Kb -- Windows Installer for Python 2.3 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.49.win32-py2.4.exe biopython-1.49.win32-py2.4.exe] 1,115 Kb -- Windows Installer for Python 2.4 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.49.win32-py2.5.exe biopython-1.49.win32-py2.5.exe] 1,115 Kb -- Windows Installer for Python 2.5 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.49b.tar.gz biopython-1.49b.tar.gz] 4,331 Kb (November 7, 2008)
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* [http://biopython.org/DIST/biopython-1.49b.zip biopython-1.49b.zip] 4,780 Kb
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* [http://biopython.org/DIST/biopython-1.49b.win32-py2.3.exe biopython-1.49b.win32-py2.3.exe] 1,109 Kb -- Windows Installer for Python 2.3 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.49b.win32-py2.4.exe biopython-1.49b.win32-py2.4.exe] 1,113 Kb -- Windows Installer for Python 2.4 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.49b.win32-py2.5.exe biopython-1.49b.win32-py2.5.exe] 1,114 Kb -- Windows Installer for Python 2.5 and NumPy 1.1
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Please note that Biopython 1.48 and older require the Numeric library, not its replacement NumPy.  Windows installers for Python 2.4 and older are available from the [http://numpy.scipy.org/#older_array Numerical Python] website. A Windows installer for Numeric 24.2 for Python 2.5 is available here: [http://biopython.org/DIST/Numeric-24.2.win32-py2.5.exe Numeric-24.2.win32-py2.5.exe] 446 Kb
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Please note that Biopython 1.48 and older used [http://www.egenix.com/www2002/python/eGenix-mx-Extensions-v2.x.html/ mxTextTools 2.0] in some of the parsers.  There were a few niggles with mxTextTools 3.0, so ideally install the older mxTextTools 2.0.
 +
 
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* [http://biopython.org/DIST/biopython-1.48.tar.gz biopython-1.48.tar.gz] 4,051 Kb (September 8, 2008)
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* [http://biopython.org/DIST/biopython-1.48.zip biopython-1.48.zip] 4,542 Kb
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* [http://biopython.org/DIST/biopython-1.48.win32-py2.3.exe biopython-1.48.win32-py2.3.exe] 1,226 Kb
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* [http://biopython.org/DIST/biopython-1.48.win32-py2.4.exe biopython-1.48.win32-py2.4.exe] 1,254 Kb
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* [http://biopython.org/DIST/biopython-1.48.win32-py2.5.exe biopython-1.48.win32-py2.5.exe] 1,254 Kb
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* [http://biopython.org/DIST/biopython-1.47.tar.gz biopython-1.47.tar.gz] 4,018 Kb (July 5, 2008)
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* [http://biopython.org/DIST/biopython-1.47.zip biopython-1.47.zip] 4,528 Kb
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* [http://biopython.org/DIST/biopython-1.47.win32-py2.3.exe biopython-1.47.win32-py2.3.exe] 1,207 Kb
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* [http://biopython.org/DIST/biopython-1.47.win32-py2.4.exe biopython-1.47.win32-py2.4.exe] 1,236 Kb
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* [http://biopython.org/DIST/biopython-1.47.win32-py2.5.exe biopython-1.47.win32-py2.5.exe] 1,236 Kb
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* [http://biopython.org/DIST/biopython-1.46.tar.gz biopython-1.46.tar.gz] 3,926 Kb (June 29, 2008)
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* [http://biopython.org/DIST/biopython-1.46.zip biopython-1.46.zip] 4,426 Kb
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* [http://biopython.org/DIST/biopython-1.46.win32-py2.3.exe biopython-1.46.win32-py2.3.exe] 1,206 Kb
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* [http://biopython.org/DIST/biopython-1.46.win32-py2.4.exe biopython-1.46.win32-py2.4.exe] 1,235 Kb
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* [http://biopython.org/DIST/biopython-1.46.win32-py2.5.exe biopython-1.46.win32-py2.5.exe] 1,235 Kb
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* [http://biopython.org/DIST/biopython-1.45.tar.gz biopython-1.45.tar.gz] 3,886 Kb (March 22, 2008)
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* [http://biopython.org/DIST/biopython-1.45.zip biopython-1.45.zip] 4,395 Kb
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* [http://biopython.org/DIST/biopython-1.45.win32-py2.3.exe biopython-1.45.win32-py2.3.exe] 1,113 Kb
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* [http://biopython.org/DIST/biopython-1.45.win32-py2.4.exe biopython-1.45.win32-py2.4.exe] 1,141 Kb
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* [http://biopython.org/DIST/biopython-1.45.win32-py2.5.exe biopython-1.45.win32-py2.5.exe] 1,142 Kb
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* [http://biopython.org/DIST/biopython-1.44.tar.gz biopython-1.44.tar.gz] 3,750 Kb (October 28, 2007)
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* [http://biopython.org/DIST/biopython-1.44.zip biopython-1.44.zip] 4,243 Kb
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* [http://biopython.org/DIST/biopython-1.44.win32-py2.3.exe biopython-1.44.win32-py2.3.exe] 1,091 Kb
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* [http://biopython.org/DIST/biopython-1.44.win32-py2.4.exe biopython-1.44.win32-py2.4.exe] 1,116 Kb
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* [http://biopython.org/DIST/biopython-1.44.win32-py2.5.exe biopython-1.44.win32-py2.5.exe] 1,116 Kb
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* [http://biopython.org/DIST/biopython-1.43.tar.gz biopython-1.43.tar.gz] 3,778 Kb (March 17, 2007)
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* [http://biopython.org/DIST/biopython-1.43.zip biopython-1.43.zip] 4,271 Kb
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* [http://biopython.org/DIST/biopython-1.43.win32-py2.3.exe biopython-1.43.win32-py2.3.exe] 1,104 Kb
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* [http://biopython.org/DIST/biopython-1.43.win32-py2.4.exe biopython-1.43.win32-py2.4.exe] 1,108 Kb
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* [http://biopython.org/DIST/biopython-1.43.win32-py2.5.exe biopython-1.43.win32-py2.5.exe] 1,109 Kb
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* [http://biopython.org/DIST/biopython-1.42.tar.gz biopython-1.42.tar.gz] 3,841 Kb (July 16, 2006)
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* [http://biopython.org/DIST/biopython-1.42.zip biopython-1.42.zip] 4,399 Kb
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* [http://biopython.org/DIST/biopython-1.42.win32-py2.3.exe biopython-1.42.win32-py2.3.exe] 1,070 Kb
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* [http://biopython.org/DIST/biopython-1.42.win32-py2.4.exe biopython-1.42.win32-py2.4.exe] 1,074 Kb
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* [http://biopython.org/DIST/biopython-1.42.win32-py2.5.exe biopython-1.42.win32-py2.5.exe] 1,075 Kb
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* [http://biopython.org/DIST/biopython-1.41.tar.gz biopython-1.41.tar.gz] 3,719 Kb (October 28, 2005)
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* [http://biopython.org/DIST/biopython-1.41.zip biopython-1.41.zip] 4,241 Kb
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* [http://biopython.org/DIST/biopython-1.41.win32-py2.3.exe biopython-1.41.win32-py2.3.exe] 1,038 Kb
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* [http://biopython.org/DIST/biopython-1.41.win32-py2.4.exe biopython-1.41.win32-py2.4.exe] 1,042 Kb
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* [http://biopython.org/DIST/biopython-1.40b.tar.gz biopython-1.40b.tar.gz] 3,437 Kb (February 18, 2005)
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* [http://biopython.org/DIST/biopython-1.40b.zip biopython-1.40b.zip] 3,267 Kb
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* [http://biopython.org/DIST/biopython-1.40b.win32-py2.3.exe biopython-1.40b.win32-py2.3.exe] 1,019 Kb
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* [http://biopython.org/DIST/biopython-1.40b.win32-py2.4.exe biopython-1.40b.win32-py2.4.exe] 1,023 Kb
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* [http://biopython.org/DIST/biopython-1.30.tar.gz biopython-1.30.tar.gz] 3,186 Kb (May 14, 2004)
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* [http://biopython.org/DIST/biopython-1.24.tar.gz biopython-1.24.tar.gz] 3,081 Kb (February 16, 2004)
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* [http://biopython.org/DIST/biopython-1.24.zip biopython-1.24.zip] 3,623 Kb
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* [http://biopython.org/DIST/biopython-1.24.win32-py2.2.exe biopython-1.24.win32-py2.2.exe] 892 Kb
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* [http://biopython.org/DIST/biopython-1.24.win32-py2.3.exe biopython-1.24.win32-py2.3.exe] 894 Kb
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* [http://biopython.org/DIST/biopython-1.23.tar.gz biopython-1.23.tar.gz] 2,241 Kb (October 18, 2003)
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* [http://biopython.org/DIST/biopython-1.23.zip biopython-1.23.zip] 2,719 Kb
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* [http://biopython.org/DIST/biopython-1.23.win32-py2.2.exe biopython-1.23.win32-py2.2.exe] 833 Kb
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* [http://biopython.org/DIST/biopython-1.23.win32-py2.3.exe biopython-1.23.win32-py2.3.exe] 842 Kb
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* [http://biopython.org/DIST/biopython-1.22.tar.gz biopython-1.22.tar.gz] 2,214 Kb (October 9, 2003)
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* [http://biopython.org/DIST/biopython-1.22.zip biopython-1.22.zip] 2,691 Kb
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* [http://biopython.org/DIST/biopython-1.21.tar.gz biopython-1.21.tar.gz] 2,214 Kb
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* [http://biopython.org/DIST/biopython-1.21.zip biopython-1.21.zip] 2,897 Kb
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* [http://biopython.org/DIST/biopython-1.21.win32-py2.2.exe biopython-1.21.win32-py2.2.exe] 770 Kb
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* [http://biopython.org/DIST/biopython-1.21.win32-py2.3.exe biopython-1.21.win32-py2.3.exe] 832 Kb
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* [http://biopython.org/DIST/biopython-1.20.tar.gz biopython-1.20.tar.gz] 2,101 Kb (July 28, 2003)
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* [http://biopython.org/DIST/biopython-1.20.zip biopython-1.20.zip] 2,602 Kb
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* [http://biopython.org/DIST/biopython-1.10.tar.gz biopython-1.10.tar.gz] 1,811 Kb (December 17, 2002)
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* [http://biopython.org/DIST/biopython-1.10.zip biopython-1.10.zip] 2,300 Kb
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* [http://biopython.org/DIST/biopython-1.10.win32-py2.2.exe biopython-1.10.win32-py2.2.exe] 1,199 Kb
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* [http://biopython.org/DIST/biopython-1.00a4.tar.gz biopython-1.00a4.tar.gz] 1,739Kb (December 18, 2001)
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* [http://biopython.org/DIST/biopython-1.00a4.zip biopython-1.00a4.zip] 2,121Kb
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* [http://biopython.org/DIST/biopython-1.00a4.win32-py2.0.exe biopython-1.00a4.win32-py2.0.exe] 835Kb
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* [http://biopython.org/DIST/biopython-1.00a4.win32-py2.1.exe biopython-1.00a4.win32-py2.1.exe] 837Kb
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* [http://biopython.org/DIST/biopython-1.00a4.win32-py2.2.exe biopython-1.00a4.win32-py2.2.exe] 838Kb
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* [http://biopython.org/DIST/MacBiopython-1.00a4.sit MacBiopython-1.00a4.sit] 2.2Mb
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* [http://biopython.org/DIST/biopython-1.00a3.tar.gz biopython-1.00a3.tar.gz] 1,816Kb (September 3, 2001)
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* [http://biopython.org/DIST/biopython-1.00a3.zip biopython-1.00a3.zip] 2,165Kb
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* [http://biopython.org/DIST/biopython-1.00a3.win32-py2.0.exe biopython-1.00a3.win32-py2.0.exe] 583Kb
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* [http://biopython.org/DIST/biopython-1.00a3.win32-py2.1.exe biopython-1.00a3.win32-py2.1.exe] 585Kb
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* [http://biopython.org/DIST/Macbiopython-1.00a3.sit.bin Macbiopython-1.00a3.sit.bin] 1926Kb

Revision as of 11:45, 4 February 2013

Contents

Current Release - 1.60 - 25 June 2012

See also What's new.

Files

Please report any issues on our mailing lists or bug tracker.

Note we don't (yet) have official 64 bit Windows Installers - however, Christoph Gohlke has kindly made Windows 64bit installers for NumPy and Biopython (and other tools) available for testing.

Installation Instructions

For Windows we provide click-and-run installers (specific to your version of python), but you will first need to install some prerequisite software (listed below, in particular, NumPy).

Most Linux distributions will include an optional Biopython package (described below), and will take care of any prerequisite software automatically.

For Mac OS X, we recommend installing from source (see below). Under (Snow) Leopard, you will need to have installed Apple's XCode tools including the optional 10.4 SDK (check the option for 10.4 support when installing Xcode tools) which comes on DVD with the computer. For Lion, just install XCode from the Apple App Store (it is a big download).

Otherwise you typically install from source by downloading and uncompressing the archive, then running the commands:

python setup.py build
python setup.py test
sudo python setup.py install

If you have trouble, see the full installation instructions:

If you are still stuck, sign up to the Biopython mailing list and ask for help there.

Required Software

  • Python 2.5, 2.6 or 2.7 (Biopython 1.56 was the last release to officially support Python 2.4, although Biopython 1.58 should work)
  • C compiler (if compiling from source) You need a C compiler supported by distutils, gcc will work fine on UNIX-like platforms. This is not needed on Windows if using the install programs provided above. On Mac OS, we recommend you install Apple's XCode including the 10.4 SDK if offered.
  • NumPy (Numerical Python). Note that until Biopython 1.49, Biopython used the older Numeric library. We have tested NumPy 1.1 to 1.5 with Biopython.

Optional Software

For compiling Biopython:

Some parts of Biopython use the following additional python libraries:

In addition Biopython includes wrapper code for calling a number of third party command line tools including:

  • Wise2 -- for command line tool dnal
  • NCBI Standalone BLAST -- command line tool for running BLAST on your local machine
  • Clustalw -- command line tool for building sequence alignments
  • SIMCOAL2 and FDist -- command line tools for population genetics
  • EMBOSS -- lots of useful command line tools.

Easy Install

We don't officially sanction this option, but it has been reported to work fine. If you have easy_install installed on your computer, you can download and install the latest Biopython distribution by simply executing this command:

 easy_install -f http://biopython.org/DIST/ biopython

You will have to have administrator's rights to do this. On a Unix style system this is normally done by:

 sudo easy_install -f http://biopython.org/DIST/ biopython

Packages

For those of you using Linux, the easiest way to install Biopython is through your distribution's package management system. However, unless you are running a recent release of your Linux Distribution, you may find that the Biopython packages available to be a little out of date. You might want to see if there is a backport available, otherwise you will have to install Biopython from source.

Ubuntu or Debian

You should be able to install Biopython and its dependencies using the Synaptic GUI tool (on the main menu under System / Administration / Synaptic Package Manager), or at the command line using:

sudo apt-get install python-biopython

If you want the documentation and unit tests,

sudo apt-get install python-biopython-doc

And if you want to use BioSQL,

sudo apt-get install python-biopython-sql

However, this will probably not be the latest release (see Ubuntu listing here, and Debian listing here). If you want the latest version of Biopython, you will need to install it from source. However, you should be able to automatically install the build dependencies with the following command:

sudo apt-get build-dep python-biopython

Note: You may need to additionally install the NumPy package by hand, as a very out of date repository may still expect Biopython to use Numeric instead.

Fedora

Biopython is an official Fedora package (since Fedora 5). The package is named python-biopython, and can be installed using yum as root:

yum install python-biopython

or via one of the GUI package management systems such as pirut and PackageKit (available in F-9 and later).

Gentoo Linux

Gentoo's portage tree contains an ebuild (sci-biology/biopython) which builds from source. To install it, open a terminal as root and run:

emerge -va biopython 

Here is a link to Biopython at Gentoo-Portage which shows the latest versions in Gentoo's Portage tree.

Ports

FreeBSD

The most easy way of installing Biopython in FreeBSD is through the Ports Collection. If you're new to this procedure please take a look at this document. Supposing that you're familiar with this method and that you have an up-to-date ports tree, all you need to do is to execute the following commands as root:

cd /usr/ports/biology/py-biopython
make install clean

Due to the great architecture of the ports system, this simple commands will automatically fetch and install Biopython (as well as its necessary dependencies).

Old Releases

Recent releases of Biopython require NumPy (and not Numeric):

Please note that Biopython 1.48 and older require the Numeric library, not its replacement NumPy. Windows installers for Python 2.4 and older are available from the Numerical Python website. A Windows installer for Numeric 24.2 for Python 2.5 is available here: Numeric-24.2.win32-py2.5.exe 446 Kb

Please note that Biopython 1.48 and older used mxTextTools 2.0 in some of the parsers. There were a few niggles with mxTextTools 3.0, so ideally install the older mxTextTools 2.0.

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