aa92ad2e67
12 February 2023: Biopython 1.81 =============================================== This release of Biopython supports Python 3.7, 3.8, 3.9, 3.10, 3.11. It has also been tested on PyPy3.7 v7.3.5. We intend to drop Python 3.7 support. The API documentation and the `Biopython Tutorial and Cookbook` have been updated to better annotate use and application of the ``Bio.PDB.internal_coords`` module. ``Bio.Phylo`` now supports ``Alignment`` and ``MultipleSeqAlignment`` objects as input. Several improvements and bug fixes to the snapgene parser contributes by Damien Goutte-Gattat. Additionally, a number of small bugs and typos have been fixed with additions to the test suite. 18 November 2022: Biopython 1.80 ================================ This release of Biopython supports Python 3.7, 3.8, 3.9, 3.10, 3.11. It has also been tested on PyPy3.7 v7.3.5. Functions ``read``, ``parse``, and ``write`` were added to ``Bio.Align`` to read and write ``Alignment`` objects. String formatting and printing output of ``Alignment`` objects from ``Bio.Align`` were changed to support these new functions. To obtain a string showing the aligned sequence with the appropriate gap characters (as previously shown when calling ``format`` on an alignment), use ``alignment[i]``, where ``alignment`` is an ``Alignment`` object and ``i`` is the index of the aligned sequence. Because dict retains the item order by default since Python3.6, all instances of ``collections.OrderedDict`` have been replaced by either standard ``dict`` or where appropriate by ``collections.defaultsdict``. Robert Miller has updated the ``Bio.PDB.internal_coords`` module to make better use of Numpy for lossless structure assembly from dihedral angles and related internal coordinates. In addition to speeding the assembly step by ~30%, this adds distance plot support (including re-generating structures from distance plot data), coordinate space transforms for superimposing residues and their environments, a per-chain all-atom array for Atom coordinates, and optional default values for all internal coordinates. The internal coordinates module continues to support extracting dihedral angle, bond angle and bond length (internal coordinates) data, reading/writing structure files of internal coordinates, and OpenSCAD output of structures for 3D CAD/3D printing work. The ``Bio.motifs.jaspar.db`` now returns ``tf_family`` and ``tf_class`` as a string array since the JASPAR 2018 release. The Local Composition Complexity functions from ``Bio.SeqUtils`` now uses base 4 log instead of 2 as stated in the original reference Konopka (2005), Sequence Complexity and Composition. https://doi.org/10.1038/npg.els.0005260 Append mode is now supported in ``Bio.bgzf`` (and a bug parsing blocked GZIP files with an internal empty block fixed). The experimental warning was dropped from ``Bio.phenotype`` (which was new in Biopython 1.67). Sequences now have a ``defined`` attribute that returns a boolean indicating if the underlying data is defined or not. The ``Bio.PDB`` module now includes a structural alignment module, using the combinatorial extension algorithm of Shindyalov and Bourne, commonly known as CEAlign. The module allows for two structures to be aligned based solely on their 3D conformation, ie. in a sequence-independent manner. The method is particularly powerful when the structures shared a very low degree of sequence similarity. The new module is available in ``Bio.PDB.CEAligner`` with an interface similar to other 3D superimposition modules. A new module ``Bio.PDB.qcprot`` implements the QCP superposition algorithm in pure Python, deprecating the existing C implementation. This leads to a slight performance improvement and to much better maintainability. The refactored ``qcprot.QCPSuperimposer`` class has small changes to its API, to better mirror that of ``Bio.PDB.Superimposer``. The ``Bio.PDB.PDBList`` module now allows downloading biological assemblies, for one or more entries of the wwPDB. In the ``Bio.Restriction`` module, each restriction enzyme now includes an `id` property giving the numerical identifier for the REBASE database identifier from which the enzyme object was created, and a `uri` property with a canonical `identifiers.org` link to the database, for use in linked-data representations. Add new ``gc_fraction`` function in ``SeqUtils`` and marks ``GC`` for future deprecation. Support for the old format (dating back to 2004) of the GN line in SwissProt files was dropped in ``Bio.SwissProt``. Additionally, a number of small bugs and typos have been fixed with additions to the test suite. |
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.. | ||
ad2vcf | ||
arka | ||
atac-seq | ||
azara | ||
balance-tui | ||
bcftools | ||
beagle | ||
bedtools | ||
biolibc | ||
biolibc-tools | ||
bioperl | ||
bodr | ||
bowtie2 | ||
bwa | ||
canu | ||
cdhit | ||
chemtool | ||
chip-seq | ||
clustalw | ||
coalesce | ||
coordgenlibs | ||
fasda | ||
fastDNAml | ||
fastp | ||
fastq-trim | ||
fastqc | ||
fastx-toolkit | ||
filter-fastq | ||
fluctuate | ||
gabedit | ||
generand | ||
genesplicer | ||
gffread | ||
glimmer | ||
gp | ||
gromacs | ||
hisat2 | ||
hmmer | ||
htslib | ||
igv | ||
kallisto | ||
lucy | ||
maeparser | ||
microsynteny-tools | ||
miniasm | ||
minimap2 | ||
molsketch | ||
mopac | ||
mpqc | ||
mummer | ||
ncbi-blast+ | ||
nut | ||
openbabel | ||
p5-Bio-ASN1-EntrezGene | ||
pdbalign | ||
peak-classifier | ||
phylip | ||
plink | ||
plinkseq | ||
primer3 | ||
profit | ||
puzzle | ||
py-bcbio-gff | ||
py-biopython | ||
py-cutadapt | ||
py-dna-features-viewer | ||
py-dnaio | ||
py-macs2 | ||
py-multiqc | ||
py-pydicom | ||
R-popbio | ||
racon | ||
rasmol | ||
rna-seq | ||
rna-star | ||
samtools | ||
seqtk | ||
sewer | ||
sra-tools | ||
stacks | ||
stride | ||
stringtie | ||
trimmomatic | ||
vcf-split | ||
vcf2hap | ||
vsearch | ||
xmakemol | ||
xylem | ||
Makefile |