From tra at popgen.net  Thu May 29 10:01:41 2014
From: tra at popgen.net (Tiago Antao)
Date: Thu, 29 May 2014 15:01:41 +0100
Subject: [Biopython-announce] Biopython 1.64 released
Message-ID: <20140529150141.2b9bbf51@lnx>

Source distributions and Windows installers for Biopython 1.64 are now
available from the downloads page on the official Biopython website and
from the Python Package Index (PyPI). 

This release of Biopython supports Python 2.6 and 2.7, 3.3 and also the
new 3.4 version. It is also tested on PyPy 2.0 to 2.3, and Jython
2.7b2. 

The new experimental module Bio.CodonAlign facilitates building codon
alignment and further analysis upon it. This work is from the Google
Summer of Code (GSoC) project by Zheng Ruan. 

Bio.Phylo now has tree construction and consensus modules, from on the
GSoC work by Yanbo Ye. 

Bio.Entrez will now automatically download and cache new NCBI DTD files
for XML parsing under the user's home directory (using ``~/.biopython``
on Unix like systems, and ``$APPDATA/biopython`` on Windows).

Bio.Sequencing.Applications now includes a wrapper for the samtools
command line tool.

Bio.PopGen.SimCoal now also supports fastsimcoal.

SearchIO hmmer3-text, hmmer3-tab, and hmmer3-domtab now support output
from hmmer3.1b1.

BioSQL can now use the mysql-connector package (available for Python 2,
3 and PyPy) as an alternative to MySQLdb (Python 2 only) to connect to
a MySQL database.

Many thanks to the Biopython developers and community for making this
release possible, especially the following contributors:

Chunlei Wu
Edward Liaw
Eric Talevich
Leighton Pritchard
Manlio Calvi
Markus Piotrowski
Melissa Gymrek
Michiel de Hoon
Nigel Delaney
Peter Cock
Saket Choudhary
Tiago Antao
Vincent Davis
Wibowo 'Bow' Arindrarto
Yanbo Ye
Zheng Ruan

From tra at popgen.net  Thu May 29 14:01:41 2014
From: tra at popgen.net (Tiago Antao)
Date: Thu, 29 May 2014 15:01:41 +0100
Subject: [Biopython-announce] Biopython 1.64 released
Message-ID: <20140529150141.2b9bbf51@lnx>

Source distributions and Windows installers for Biopython 1.64 are now
available from the downloads page on the official Biopython website and
from the Python Package Index (PyPI). 

This release of Biopython supports Python 2.6 and 2.7, 3.3 and also the
new 3.4 version. It is also tested on PyPy 2.0 to 2.3, and Jython
2.7b2. 

The new experimental module Bio.CodonAlign facilitates building codon
alignment and further analysis upon it. This work is from the Google
Summer of Code (GSoC) project by Zheng Ruan. 

Bio.Phylo now has tree construction and consensus modules, from on the
GSoC work by Yanbo Ye. 

Bio.Entrez will now automatically download and cache new NCBI DTD files
for XML parsing under the user's home directory (using ``~/.biopython``
on Unix like systems, and ``$APPDATA/biopython`` on Windows).

Bio.Sequencing.Applications now includes a wrapper for the samtools
command line tool.

Bio.PopGen.SimCoal now also supports fastsimcoal.

SearchIO hmmer3-text, hmmer3-tab, and hmmer3-domtab now support output
from hmmer3.1b1.

BioSQL can now use the mysql-connector package (available for Python 2,
3 and PyPy) as an alternative to MySQLdb (Python 2 only) to connect to
a MySQL database.

Many thanks to the Biopython developers and community for making this
release possible, especially the following contributors:

Chunlei Wu
Edward Liaw
Eric Talevich
Leighton Pritchard
Manlio Calvi
Markus Piotrowski
Melissa Gymrek
Michiel de Hoon
Nigel Delaney
Peter Cock
Saket Choudhary
Tiago Antao
Vincent Davis
Wibowo 'Bow' Arindrarto
Yanbo Ye
Zheng Ruan