Source distributions and Windows installers for Biopython 1.68 are now available from the downloads page on the official Biopython website, and the release is also on the Python Package Index (PyPI).
This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5, but this will be our final release to run on Python 2.6. It has also been tested on PyPy 5.0, PyPy3 version 2.4, and Jython 2.7.
Bio.PDB has been extended to parse the RSSB’s new binary Macromolecular Transmission Format (MMTF, see http://mmtf.rcsb.org), in addition to the mmCIF and PDB file formats (contributed by Anthony Bradley). This requires an optional external dependency on the mmtf-python library.
Module Bio.pairwise2 has been re-written (contributed by Markus Piotrowski). It is now faster, addresses some problems with local alignments, and also now allows gap insertions after deletions, and vice versa, inspired by the preprint from Flouri et al.
The two sample graphical tools SeqGui (Sequence Graphical User Interface) and xbbtools were rewritten (SeqGui) or updated (xbbtools) using the tkinter library (contributed by Markus Piotrowski). SeqGui allows simple nucleotide transcription, back-transcription and translation into amino acids using Bio.Seq internally, offering of the NCBI genetic codes supported in Biopython. xbbtools is able to open Fasta formatted files, does simple nucleotide operations and translations in any reading frame using one of the NCBI genetic codes. In addition, it supports standalone Blast installations to do local Blast searches.
New NCBI genetic code table 26 (Pachysolen tannophilus Nuclear Code) has been added to Bio.Data (and the translation functionality), and table 11 is now also available under the alias Archaeal.
In line with NCBI website HTTPS changes, Biopython now uses HTTPS rather than HTTP to connect to the NCBI Entrez and QBLAST API.
Additionally, a number of small bugs have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8 and best practice standard coding style.
Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:
- Anthony Bradley (first contribution)
- Ben Fulton
- Carlos Pena
- Connor T. Skennerton
- Iddo Friedberg
- Kai Blin
- Kristian Davidsen (first contribution)
- Markus Piotrowski
- Olivier Morelle (first contribution)
- Peter Cock
- Tiago Antao
- Travis Wrightsman
- Uwe Schmitt (first contribution)
- Xiaoyu Zhuo (first contribution)
Thank you all.
P.S. You can follow @Biopython on Twitter
$ md5sum biopython-1.68.*
$ shasum -a 256 biopython-1.68.*
Updated 29 August 2016 to include the Python 3.5 installer checksums.