Biopython for Windows (x32 bit) full changelog
Biopython for Windows (x32 bit) 1.83
released Feb 7, 2024 (New Release)
Biopython for Windows (x32 bit) 1.81
released Feb 12, 2023 (New Release)
Biopython for Windows (x32 bit) 1.80
released Nov 18, 2022 (New Release)
Biopython for Windows (x32 bit) 1.79
released Jun 3, 2021 (New Release)
Biopython for Windows (x32 bit) 1.66
released Nov 2, 2015 (New Release)
Further work on the Bio.KEGG and Bio.Graphics modules now allows drawing KGML
pathways with transparency.
The Bio.SeqIO "abi" parser now decodes almost all the documented fields used
by the ABIF instruments - including the individual color channels.
Bio.PDB now has a QCPSuperimposer module using the Quaternion Characteristic
Polynomial algorithm for superimposing structures. This is a fast alternative
to the existing SVDSuperimposer code using singular value decomposition.
Bio.Entrez now implements the NCBI Entrez Citation Matching function
(ECitMatch), which retrieves PubMed IDs (PMIDs) that correspond to a set of
input citation strings.
Bio.Entrez.parse(...) now supports NCBI XML files using XSD schemas, which
will be downloaded and cached like NCBI DTD files.
A subtle bug in how multi-part GenBank/EMBL locations on the reverse strand
were parsed into CompoundLocations was fixed: complement(join(...)) as used
by NCBI worked, but join(complement(...),complement(...),...)
pathways with transparency.
The Bio.SeqIO "abi" parser now decodes almost all the documented fields used
by the ABIF instruments - including the individual color channels.
Bio.PDB now has a QCPSuperimposer module using the Quaternion Characteristic
Polynomial algorithm for superimposing structures. This is a fast alternative
to the existing SVDSuperimposer code using singular value decomposition.
Bio.Entrez now implements the NCBI Entrez Citation Matching function
(ECitMatch), which retrieves PubMed IDs (PMIDs) that correspond to a set of
input citation strings.
Bio.Entrez.parse(...) now supports NCBI XML files using XSD schemas, which
will be downloaded and cached like NCBI DTD files.
A subtle bug in how multi-part GenBank/EMBL locations on the reverse strand
were parsed into CompoundLocations was fixed: complement(join(...)) as used
by NCBI worked, but join(complement(...),complement(...),...)
Biopython for Windows (x32 bit) 1.62
released Feb 5, 2013 (New Release)
Biopython for Windows (x32 bit) 1.61
released Feb 5, 2013 (New Release)
enomeDiagram has three new sigils (shapes to illustrate features). OCTO shows
an octagonal shape, like the existing BOX sigil but with the corners cut off.
JAGGY shows a box with jagged edges at the start and end, intended for things
like NNNNN regions in draft genomes. Finally BIGARROW is like the existing
ARROW sigil but is drawn straddling the axis. This is useful for drawing
vertically compact figures where you do not have overlapping genes.
New module Bio.Graphics.ColorSpiral can generate colors along a spiral path
through HSV color space. This can be used to make arbitrary 'rainbow' scales,
for example to color features or cross-links on a GenomeDiagram figure.
The Bio.SeqIO module now supports reading sequences from PDB files in two
different ways. The quot;pdb-atomquot; format determines the sequence as it appears in
the structure based on the atom coordinate section of the file (via Bio.PDB,
so NumPy is currently required for this).
an octagonal shape, like the existing BOX sigil but with the corners cut off.
JAGGY shows a box with jagged edges at the start and end, intended for things
like NNNNN regions in draft genomes. Finally BIGARROW is like the existing
ARROW sigil but is drawn straddling the axis. This is useful for drawing
vertically compact figures where you do not have overlapping genes.
New module Bio.Graphics.ColorSpiral can generate colors along a spiral path
through HSV color space. This can be used to make arbitrary 'rainbow' scales,
for example to color features or cross-links on a GenomeDiagram figure.
The Bio.SeqIO module now supports reading sequences from PDB files in two
different ways. The quot;pdb-atomquot; format determines the sequence as it appears in
the structure based on the atom coordinate section of the file (via Bio.PDB,
so NumPy is currently required for this).
Biopython for Windows (x32 bit) 1.60
released Jun 25, 2012 (New Release)
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. This uses Python's zlib library
internally, and provides a simple interface like Python's gzip library.
Using this the Bio.SeqIO indexing functions now support BGZF compressed
sequence files.
The GenBank/EMBL parser will now give a warning on unrecognised feature
locations and continue parsing (leaving the feature's location as None).
Previously it would abort with an exception, which was often unhelpful.
The Bio.PDB.MMCIFParser is now compiled by default (but is still not
available under Jython, PyPy or Python 3).
The SFF parser in Bio.SeqIO now decodes Roche 454 'universal accession
number' 14 character read names, which encode the timestamp of the run,
the region the read came from, and the location of the well.
Zip Format), a variant of GZIP with efficient random access, most commonly
used as part of the BAM file format. This uses Python's zlib library
internally, and provides a simple interface like Python's gzip library.
Using this the Bio.SeqIO indexing functions now support BGZF compressed
sequence files.
The GenBank/EMBL parser will now give a warning on unrecognised feature
locations and continue parsing (leaving the feature's location as None).
Previously it would abort with an exception, which was often unhelpful.
The Bio.PDB.MMCIFParser is now compiled by default (but is still not
available under Jython, PyPy or Python 3).
The SFF parser in Bio.SeqIO now decodes Roche 454 'universal accession
number' 14 character read names, which encode the timestamp of the run,
the region the read came from, and the location of the well.
Biopython for Windows (x32 bit) 1.58
released Aug 18, 2011 (New Release)
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 and write support for the SeqXML, a simple XML
format offering basic annotation support. See Schmitt et al (2011) in
Briefings in Bioinformatics, http://dx.doi.org/10.1093/bib/bbr025
Bio.SeqIO now includes read support for ABI files (quot;Sangerquot; capillary
sequencing trace files, containing called sequence with PHRED qualities).
The Bio.AlignIO quot;fasta-m10quot; parser was updated to cope with the >>><<< lines
as used in Bill Pearson's FASTA version 3.36, without this fix the parser
would only return alignments for the first query sequence.
The Bio.AlignIO quot;phylipquot; parser and writer now treat a dot/period in the
sequence as an error, in line with the official PHYLIP specification.
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 and write support for the SeqXML, a simple XML
format offering basic annotation support. See Schmitt et al (2011) in
Briefings in Bioinformatics, http://dx.doi.org/10.1093/bib/bbr025
Bio.SeqIO now includes read support for ABI files (quot;Sangerquot; capillary
sequencing trace files, containing called sequence with PHRED qualities).
The Bio.AlignIO quot;fasta-m10quot; parser was updated to cope with the >>><<< lines
as used in Bill Pearson's FASTA version 3.36, without this fix the parser
would only return alignments for the first query sequence.
The Bio.AlignIO quot;phylipquot; parser and writer now treat a dot/period in the
sequence as an error, in line with the official PHYLIP specification.
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