Biopython

Developed an international team of developers it's a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future works in bioinformatics.

What is new in this release:

• 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.

What is new in version 1.63:

• Now uses the Python 3 style built-in next function in place of the Python 2 style iterators' .next() method.
• The current version removed the requirement of the 2to3 library.

What is new in version 1.62:

• First release of Biopython which officially supports Python 3.

What is new in version 1.60:

• New module Bio.bgzf supports reading and writing BGZF files (Blocked GNU Zip Format), a variant of GZIP with efficient random access, most commonly used as part of the BAM file format and in tabix.
• The GenBank/EMBL parser will now give a warning on unrecognized feature locations and continue parsing (leaving the feature's location as None).
• The Bio.PDB.MMCIFParser is now compiled by default (but is still not available under Jython, PyPy or Python 3).

What is new in version 1.59:

• New module Bio.TogoWS offers a wrapper for the TogoWS REST API.
• The NCBI Entrez Fetch function Bio.Entrez.efetch has been updated to handle the NCBI's stricter handling of multiple ID arguments in EFetch 2.0.

What is new in version 1.58:

• A new interface and parsers for the PAML (Phylogenetic Analysis by Maximum Likelihood) package of programs, supporting codeml, baseml and yn00 as well as a Python re-implementation of chi2 was added as the Bio.Phylo.PAML module.
• Bio.SeqIO now includes read support for ABI files ("Sanger" capillary sequencing trace files, containing called sequence with PHRED qualities).
• The Bio.AlignIO "fasta-m10" parser was updated to cope with the marker lines as used in Bill Pearson's FASTA version 3.36.

What is new in version 1.57:

• Biopython can now be installed with pip.

What is new in version 1.56:

• The Bio.SeqIO module has been updated to support protein EMBL files (used for the patents database), IMGT files (a variant of the EMBL file format, with help from Uri Laserson), and UniProt XML files.

What is new in version 1.55:

• A lot of work has been towards Python 3 support (via the 2to3 script), but unless we broke something you shouldn't notice any changes.
• In terms of new features, the most noticeable highlight is that the command line tool application wrapper classes are now executable, which should make it much easier to call external tools.

Requirements:

• Python 2.6 or higher