This file provides documentation for modules in Biopython that have been moved or deprecated in favor of other modules. This provides some quick and easy to find documentation about how to update your code to work again. Python releases go first, then code (modules, methods, functions). Python ====== Python 3.9 ---------- No longer supported as of Release 1.86, having triggered a deprecation warning as of Release 1.84. First supported in release 1.79, although it was mostly working in 1.78. Python 3.8 ---------- First supported in release 1.75. Support deprecated as of Release 1.83, and no longer supported as of Release 1.84. Python 3.7 ---------- No longer supported as of Release 1.82. First supported in release 1.73. Python 3.6 ---------- No longer supported as of Release 1.80, having triggered a deprecation warning as of release 1.79. First supported in release 1.69. Python 3.5 ---------- No longer supported as of Release 1.77. First supported in release 1.66. Python 3.4 ---------- No longer supported as of Release 1.75, having triggered a deprecation warning in release 1.74. First supported in release 1.64. Python 3.3 ---------- No longer supported as of Release 1.70, having triggered a warning with release 1.67 onwards. Python 3.0, 3.1, 3.2 -------------------- Never officially supported, these triggered a warning in Release 1.62 recommending Python 3.3 or later. As of Biopython Release 1.63 onwards, installation simply aborts with a error message. Python 2.7 ---------- No longer supported as of Release 1.77 (2020, in line with end-of-life or sunset date for Python 2.7 itself), having triggered a warning in prior releases. Jython ------ No longer supported as of Release 1.77 with the end of Python 2 support. Biopython was mostly working under Jython 2.7.0, but support for Jython was deprecated as of Release 1.70. Biopython modules, methods, functions ===================================== Bio.SeqIO.FastaIO ----------------- Parsing a FASTA file using Bio.SeqIO.parse with ``format='fasta'`` interprets lines before the first line starting with '>' as comments and skips them. To be consistent with the most common interpretation of the FASTA file format, the use of such comment lines at the beginning of the FASTA file was deprecated in Biopython Release 1.85. As an alternative, you can use ``format='fasta-pearson'`` to specify the FASTA file format as defined by William Pearson's FASTA aligner program, allowing for comment lines at the top of the FASTA file (lines anywhere in the file starting by ';' are also regarded as comment lines and skipped). Another option is to use ``format='fasta-blast'``; this follows the FASTA file format accepted by BLAST, treating any lines starting with '#', ';', or '!' as comment lines and ignoring them. The functions ``as_fasta`` and ``as_fasta_2line`` in ``Bio.SeqIO.FastaIO`` were deprecated in release 1.86. Please use ``format(record, "fasta")`` or ``format(record, "fasta-2line")`` instead. Bio.SeqIO.qualityIO ------------------- The functions ``as_fastq``, ``as_fastq_solexa``, ``as_fastq_illumina``, and ``as_qual`` in ``Bio.SeqIO.QualityIO`` were deprecated in release 1.86. Please use ``format(record, "fastq")``, ``format(record, "fastq-solexa")``, ``format(record, "fastq-illumina")``, or ``format(record, "qual")`` instead. Bio.SeqIO.TabIO ------------------- The function ``as_tab`` in ``Bio.SeqIO.TabIO`` was deprecated in release 1.86. Please use ``format(record, "tab")`` instead. Bio.SeqIO.UniprotIO ------------------- Parsing a UniProt XML file opened in text mode (if the file was opened using ``open("myuniprotfile.xml")``) was deprecated in Release 1.85, as this may lead to garbled characters. Please open the file in binary mode (as in ``open("myuniprotfile.xml", "rb")``), or let ``Bio.SeqIO.parse`` take care of opening and closing files by passing the file name instead of a file handle. Bio.Entrez ---------- The ``egquery`` function wrapping the NCBI EGQuery (Entrez Global Query) API was deprecated in Release 1.84. The API has stopped working and the NCBI said this API was no longer being maintained. Bio.SCOP -------- The ``search`` function was deprecated in Release 1.84, and removed in Release 1.86. The CGI API this wrapped is no longer available since SCOP moved to the EBI website. Bio.AlignInfo ------------- The ``pos_specific_score_matrix`` method of the ``SummaryInfo`` class and the ``PSSM`` class were deprecated in release 1.82, and removed in release 1.85. The ``SummaryInfo`` class itself was deprecated in release 1.86. As an alternative, please use the ``alignment`` property of a ``MultipleSeqAlignment`` object to obtains a new-style ``Alignment`` object, and use it to create a ``Bio.motifs.Motif`` object. For example, >>> alignment = msa.alignment >>> from Bio.motifs import Motif >>> motif = Motif('ACGT', alignment) >>> counts = motif.counts The ``counts`` object contains the same information as the PSSM returned by ``pos_specific_score_matrix``, but note that the indices are reversed: >>> counts[letter][i] == pssm[index][letter] True The ``information_content`` method and the ``ic_vector`` attribute of the ``SummaryInfo`` class were deprecated in release 1.82, and removed in release 1.86. As an alternative, please use the ``relative_entropy`` attribute of the ``motif`` instance (see above); it contains the same values as the ``ic_vector`` attribute, while ``sum(relative_entropy)`` is equal to the value returned by ``information_content``. The ``replacement_dictionary`` method of the ``SummaryInfo`` class was deprecated in release 1.82, and removed in release 1.86. As an alternative, please use the ``alignment`` property of the ``MultipleSeqAlignment`` object to obtain a new-style ``Alignment`` object, and use its ``substitutions`` attribute to obtain the replacement dictionary: >>> alignment = msa.alignment >>> dictionary = alignment.substitutions If the multiple sequence alignment object ``msa`` was obtained using ``Bio.AlignIO``, then you can obtain a new-style ``Alignment`` object directly by using ``Bio.Align.read`` instead of ``Bio.AlignIO.read``, or ``Bio.Align.parse`` instead of ``Bio.AlignIO.parse``. The ``dumb_consensus`` and ``gap_consensus`` methods of the ``SummaryInfo`` class were deprecated in release 1.82, and removed in release 1.86. The ``print_info_content`` function in ``Bio.Align.AlignInfo`` was deprecated in release 1.82, and removed in release 1.86. Bio.kNN ------- Deprecated in release 1.82, and removed in release 1.86. Consider using scikit-learn instead. Bio.LogisticRegression ---------------------- Deprecated in release 1.82, and removed in release 1.86. Consider using scikit-learn instead. Bio.NaiveBayes -------------- Deprecated in release 1.82, and removed in release 1.86. Consider using skikit-learn instead. Bio.MaxEntropy -------------- Deprecated in release 1.82, and removed in release 1.86. Consider using scikit-learn instead. Bio.MarkovModel --------------- Deprecated in release 1.82, and removed in release 1.86. Consider using hmmlearn (https://pypi.org/project/hmmlearn/) instead. Bio.HMM ------- The `Bio.HMM.DynamicProgramming`, `Bio.HMM.Trainer`, `Bio.HMM.MarkovModel`, and `Bio.HMM.Utilities` modules were deprecated in release 1.82, and removed in release 1.86. Consider using hmmlearn (https://pypi.org/project/hmmlearn/) instead. Bio.PDB.Polypeptide ------------------- Functions ``three_to_one`` and ``one_to_three`` were deprecated in Release 1.80 and removed in Release 1.82. Please use the dictionary ``nucleic_letters_3to1`` instead, available from this module but defined in ``Bio.Data.PDBData``. Bio.Data.SCOPData ----------------- Deprecated in release 1.80, and removed in release 1.82. Please use ``Bio.Data.PDBData`` instead. Bio.Application and the command line wrappers using it ------------------------------------------------------ Declared obsolete in release 1.79, deprecated in release 1.82, and removed in release 1.86. Please use the standard library subprocess module directly instead. Bio.Index --------- Deprecated in release 1.75, removed in release 1.77. Was not used anywhere in Biopython. Bio.Crystal ----------- Declared obsolete in release 1.75, deprecated in release 1.76, removed in release 1.79. PDB NDB files can be opened with Bio.PDB. Bio.motifs ---------- ``Bio.motifs.mast`` plain-text parsing deprecated in favor of XML parsing as of release 1.74. Also affects ``Bio.motifs.read`` and ``Bio.motifs.parse`` for the ``mast`` format. The ``format`` method of the ``Motif`` class in ``Bio.motifs`` was deprecated in release 1.77, in favor of a ``__format__`` method that can be used from the ``format`` built-in function. This decision was reversed in release 1.79. The ``search`` method of the ``Instances`` class in ``Bio.motifs`` was deprecated in release 1.82, and removed in release 1.86. Instead of ``instances.search(sequence)``, ``sequence.search(instances)`` can be used, where sequence is a Seq object. This allows instances to have different lengths. The ``version`` parameter of the ``weblogo`` method of the ``Motif`` class in ``Bio.motifs`` was deprecated in release 1.83, and removed in release 1.86. The ``Instances`` class and the ``instances`` argument of the ``Motif`` class initializer in ``Bio.motifs`` were deprecated in release 1.82, and removed in release 1.86. Instead of >>> from Bio.motifs import Instances >>> instances = Instances([Seq('ACGT'), Seq('ACCT'), Seq('AAGT')]) >>> motif = Motif(alphabet='ACGT', instances=instances) please use >>> from Bio.Align import Alignment >>> alignment = Alignment([Seq('ACGT'), Seq('ACCT'), Seq('AAGT')]) >>> motif = Motif(alphabet='ACGT', alignment=alignment) The ``instances`` attribute of the ``Motif`` class in ``Bio.motifs`` was deprecated in release 1.82, and removed in release 1.86. Instead of ``mymotif.instances``, please use ``mymotif.alignment.sequences``. The ``Instance`` class in ``Bio.motifs.meme`` was deprecated in release 1.85. This class is a subclass from ``Seq``, but does not provide any additional capabilities. Please use a ``Seq`` object instead. Bio.Restriction.RanaConfig -------------------------- Removed in Biopython 1.74 without explicit deprecation period. RanaConfig was a configuration file containing some constants for Bio.Restriction.PrintFormat and ranacompiler.py, a script to update Bio.Restriction.Restriction_Dictionary, and which is not part of the Biopython installation. The constants were implemented in the respective modules. Bio.Alphabet ------------ Declared obsolete in Biopython release 1.74, and removed from Biopython in release 1.78. This module defined an ``Alphabet`` class and various subclasses, which were used as attributes to ``Seq`` and objects to describe how the individual characters in the sequence string should be interpreted. For example, a string "AGTACACTGGT" could be a DNA sequence or a protein sequence that happens to be rich in Alanines, Glycines, Cysteines and Threonines. However, as the exact definition of the alphabet and its purpose remained unclear, this class was removed from Biopython. Starting with Biopython 1.78, the molecule type, if specified in the input file, is stored by the ``SeqIO`` parser as ``molecule_type`` in the annotations of each ``SeqRecord``. We urge users to use this attribute with caution, as the molecule type means different things in different sequence file formats, and in a sense the interpretation of ``molecule_type`` can still be ambiguous. Bio.ExPASy.sprot_search_ful and ExPASy.sprot_search_de ------------------------------------------------------ These two functions were labelled as broken in Release 1.70, and removed in Release 1.73, since the underlying web-server API no longer exists. Bio.GA ------ This was deprecated in Biopython 1.70, and removed in Release 1.73. Please consider using a dedicated genetic algorithm library like DEAP instead. Bio.NeuralNetwork ----------------- This was deprecated in Biopython 1.70, and removed in Release 1.73. Please consider using a dedicated machine learning library like scikit-learn or TensorFlow instead. Bio.Phylo.CDAOIO.CDAOError -------------------------- This exception was deprecated as of Release 1.70 as it was no longer used within Biopython, and removed in Release 1.75. Bio.DocSQL ---------- This was deprecated in Biopython 1.69, and removed in Release 1.71. Bio.CodonAlign -------------- This new experimental module included in Biopython 1.64 was renamed to Bio.codonalign in Biopython 1.65 to follow PEP8 module naming rules. Bio.SeqRecord ------------- Creating a SeqRecord with a plain string as the seq argument was deprecated in release 1.82, and removed in release 1.86. A TypeError will be raised if seq is not a Seq or MutableSeq object. Bio.SeqRecord equality ---------------------- As of Release 1.67, the SeqRecord objects (and their subclasses) no longer use the default Python object comparison. Instead they will raise an exception if you try to compare them. For backward compatibility and/or to explicitly use object comparison, please use id(record1) == id(record2) instead. Otherwise please test whichever specific attributes you are interested in explicitly, for example record1.id == record2.id or record1.seq == record.seq (see also the note below about sequence equality). Bio.Seq sequence equality ------------------------- As of Release 1.65, the Seq and MutableSeq objects (and their subclasses) use string-like equality testing and hashing (ignoring any difference in alphabet except to issue warnings). Prior releases used Python's object comparison. Warnings of this change were first added in Release 1.54 (May 2010), with hash warnings present from Release 1.62 (August 2013) to Release 1.76 (December 2019). For backward compatibility and/or to silence warnings about this, please use explicit string comparison, str(seq1) == str(seq2), or object comparison, id(seq1) == id(seq2), as required. Bio.Seq.Seq.tostring() and Bio.Seq.MutableSeq.tostring() -------------------------------------------------------- Deprecated in release 1.64, and removed in release 1.73. You should now use str(Bio.Seq.Seq) or str(Bio.Seq.MutableSeq) instead of the tostring() methods. Bio.Seq.Seq.tomutable() and Bio.Seq.MutableSeq.toseq() ------------------------------------------------------ Deprecated in release 1.79, removed in release 1.81. Instead of myseq.tomutable() or mymutableseq.toseq(), you should now use Bio.Seq.MutableSeq(myseq) or Bio.Seq.Seq(mymutableseq), respectively. Bio.Seq.Seq.ungap() ------------------- Declared obsolete in release 1.79, deprecated in release 1.80, and removed in release 1.82. Instead of myseq.ungap(), please use myseq.replace("-", ""). Bio.Seq.UnknownSeq ------------------ Deprecated in release 1.79, and removed in release 1.81. Instead of ``UnknownSeq(length)``, please use ``Seq(None, length=length)``. Note that the sequence contents of a ``Seq`` object constructed in this way is considered to be unknown, and any attempt to access the sequence contents (for example, by calling ``print`` on the object) will result in an ``UndefinedSequenceError``. Bio.Seq: Functions and methods ``complement`` and ``reverse_complement`` ------------------------------------------------------------------------ Starting from release 1.82, the ``inplace`` argument of ``complement`` and ``reverse_complement`` in ``Bio.Seq`` always default to ``False`` both for ``Seq`` and ``MutableSeq`` objects. To modify a ``MutableSeq`` in-place, use ``inplace=True``. Iterator .next() methods ------------------------ The .next() method defined for any Biopython iterator is deprecated as of Biopython 1.63 under Python 2 (and not present on Python 3). Please replace my_iterator.next() with next(my_iterator) using the new built-in function next() instead. Python 2 support and the remaining next methods were removed in release 1.77. Bio.SVDSuperimposer ------------------- As of Release 1.63, the main class (confusingly also called) SVDSuperimposer is best imported as follows: >>> from Bio.SVDSuperimposer import SVDSuperimposer >>> super_imposer = SVDSuperimposer() This short form also works on older releases. The longer even more confusing historical alternatives dependent on the double module name no longer work, e.g. you can no longer do this: >>> from Bio.SVDSuperimposer.SVDSuperimposer import SVDSuperimposer >>> super_imposer = SVDSuperimposer() Bio.PDB.Vector (the module) --------------------------- Due to a long standing name shadowing problem, ``Bio.PDB.Vector`` was both a class and a module, which defined the class and various other functions imported to the ``Bio.PDB`` namespace. As of Release 1.70, the module has been renamed ``Bio.PDB.vectors``, leaving ``Bio.PDB.Vector`` to unambiguously mean the class. This is in line with the PEP8 naming conventions. A deprecated compatibility stub was left in place so that any imports via the old module name will work but raise a warning. This compatibility stub was removed in Release 1.74. We expect this to have no impact for the majority of users, unless you do something like ``from Bio.PDB.Vector import calc_dihedral`` in which case use ``from Bio.PDB import calc_dihedral`` (which will work on older versions of Biopython as well). Bio.PDB.Residue --------------- The ``get_atom`` and ``sort`` methods of the ``Residue`` class were deprecated in Release 1.71 and 1.70 respectively, and removed in Release 1.79. Bio.PDB.ResidueDepth -------------------- Use of the ``PDB_TO_XYZR`` bash script was removed from ``get_surface`` in Release 1.79. Bio.PDB.QCPSuperimposer ----------------------- The ``Bio.PDB.QCPSuperimposer`` module was deprecated in release 1.80, and removed in release 1.82. Please use the ``Bio.PDB.qcprot`` module instead. Bio.SeqFeature -------------- Release 1.82 unfortunately removed the ``.strand``, ``.ref``, and ``.ref_db`` attributes of the ``SeqFeature`` without a deprecation period. These attributes were restored but deprecated in Release 1.83, and removed in Release 1.86. Please use ``.location.strand`` etc instead. With the introduction of the CompoundLocation in Release 1.62, the SeqFeature attribute sub_features was deprecated. It was removed in Release 1.68. Note that in Release 1.80 the location_operator argument can no longer be used, instead do this via the CompoundLocation object. The location_operator argument was removed from the SeqFeature initializer in Release 1.82. There were multiple deprecations in Release 1.80, listed below. The deprecated code was removed in Release 1.82. * Class ``FeatureLocation`` renamed to ``SimpleLocation``, with the old name preserved for now solely for backward compatibility. * Arguments ``strand``, ``ref`` and ``ref_db`` to the ``SeqFeature`` class - set them via the location object * Unused class ``PositionGap`` - originally for very old GenBank files. * Location attributes ``location.nofuzzy_start`` and ``location.nofuzzy_end`` - use the location directly or if required ``int(location.start)`` and ``int(location.end)``. This will fail for the ``UnknownPosition`` where the nofuzzy aliases returned ``None``. * Position attribute ``.position`` returned the (left) position as an integer - use the location directly or if required ``int(position)``, however for ``OneOfPosition``, ``BetweenPosition``, and ``WithinPosition`` that will give the default position rather than the left-most (minimum) value. * Position attribute ``.extension`` returned the "width", typically zero except for ``OneOfPosition``, ``BetweenPosition``, and ``WithinPosition`` where this must be handled explicitly now. * Base class ``AbstractPosition`` was renamed to ``Position``. Bio.Motif --------- Declared obsolete with a PendingDeprecationWarning in Release 1.61, formally deprecated in Release 1.62, removed in Release 1.67. Please use the newer Bio.motifs module instead. AlignAceCommandline and CompareAceCommandline --------------------------------------------- Deprecated in release 1.62, removed in Release 1.67. An up to date version of the software cannot be obtained anymore (affects Bio.Motif and its replacement Bio.motifs). Bio.SeqIO.Interfaces -------------------- Unused class InterlacedSequenceIterator was deprecated in Release 1.61, and removed in Release 1.64. Class SequentialSequenceWriter was declared obsolete in Release 1.77, deprecated in Release 1.78, and removed in Release 1.80. Optional mode argument to the ``SequenceIterator``` and ``SequenceWriter`` initialisation was removed in Biopython 1.85. See new ``.modes`` property instead. Bio.HotRand ----------- Obsolete file Bio/HotRand.py was deprecated in Release 1.61, and removed in Release 1.64. Consider using an alternative RNG, or the Python module "randomdotorg". Bio.Search ---------- Long obsolete file Bio/Search.py was deprecated in Release 1.61, and removed in Release 1.64. Bio.Blast.NCBIStandalone ------------------------ The three functions for calling the "legacy" NCBI BLAST command line tools blastall, blastpgp and rpsblast were declared obsolete in Biopython Release 1.53, deprecated in Release 1.61, and removed in Release 1.64. Please use the BLAST+ wrappers in Bio.Blast.Applications instead. The remainder of this module is a parser for the plain text BLAST output, which was declared obsolete in Release 1.54, and deprecated in Release 1.63. The module was removed in Release 1.72 from the public API. It lives now in maintenance mode in Bio.SearchIO._legacy to preserve existing functionality. A BiopythonDeprecationWarning was added to this module in Release 1.80. The Bio.SearchIO._legacy module was removed from Biopython in Release 1.82. For some time now, both the NCBI and Biopython have encouraged people to parse the XML output instead. Bio.Blast.Applications ---------------------- NCBI "legacy" BLAST tool wrappers FastacmdCommandline, BlastallCommandline, BlastpgpCommandline and RpsBlastCommandline were declared obsolete in Release 1.53, deprecated in Release 1.61, and removed in Release 1.64, having been replaced with wrappers for the new NCBI BLAST+ tools (e.g. NcbiblastpCommandline and NcbipsiblastCommandline). This module was removed in release 1.86 as it relied on Bio.Application, which was being removed. Bio.Blast.ParseBlastTable ------------------------- The parser in ``Bio.Blast.ParseBlastTable`` for tabular output generated by NCBI blastpgp was deprecated in Biopython release 1.80, and removed in release 1.82. To parse tabular output generated by BLAST programs, please use the ``parse`` function in ``Bio.Align``. BioSQL.BioSeqDatabase --------------------- The ``remove_database`` and ``get_all_primary_ids`` methods were removed from the ``DBServer`` class in Release 1.79. The ``get_Seq_by_primary_id`` method was removed from the ``BioSeqDatabase`` class in Release 1.79. Bio.Graphics.GenomeDiagram and colour/color, centre/center ---------------------------------------------------------- GenomeDiagram originally used colour and centre (UK spelling of color and center) for argument names. As part of its integration into Biopython 1.50, this will support both colour and color, and both centre and center, to help people port existing scripts written for the standalone version of GenomeDiagram. However, these were deprecated in Release 1.55 final. Support for centre was removed in Release 1.62, and we intend to eventually remove support for colour in later releases of Biopython. Bio.Seq, Bio.MutableSeq and the data property --------------------------------------------- Direct use of the Seq object (and MutableSeq object) .data property is deprecated. As of Release 1.49, writing to the Seq object's .data property triggered a warning, and this property was made read only in Release 1.53. In Release 1.55 final, accessing the .data property of a Seq object gives a DeprecationWarning. The Seq object's .data property was removed in Release 1.61. Starting from Release 1.78, accessing the .data property of a MutableSeq object similarly gives a deprecation warning. Bio.SeqUtils ------------ Function quick_FASTA_reader was declared obsolete in Release 1.61, deprecated in Release 1.64, and removed in Release 1.67. Use function list(SimpleFastaParser(handle)) from Bio.SeqIO.FastaIO instead (but ideally convert your code to using an iterator approach). The 'title2ids' argument to FastaIterator in Bio.SeqIO.FastaIO and FastqPhredIterator in Bio.SeqIO.QualityIO was deprecated in Release 1.80, and removed in Release 1.82. Please use a generator function to modify the records returned by the parser. Function Tm_staluc in Bio.SeqUtils.MeltingTemp was deprecated in Release 1.78, and removed in Release 1.80. The modules Bio.SeqUtils.CodonUsage and Bio.SeqUtils.CodonUsageIndices were deprecated in Release 1.80, and removed in Release 1.82. Please use the new CodonAdaptationIndex class in Bio.SeqUtils instead. Note that this class has been updated to use modern Python, and may give slightly different results from the CodonAdaptationIndex class in Bio.SeqUtils.CodonUsage, as the calculation was updated to be consistent with the calculated values by Sharp & Li. Function 'GC' in Bio.SeqUtils was deprecated in Release 1.80, and removed in Release 1.82. Instead use function 'gc_fraction'. Function get_amino_acids_percent in Bio.SeqUtils.ProteinAnalysis was deprecated in Release 1.85. Use the amino_acids_percent property instead. Bio.PopGen.Async ---------------- ``Bio.PopGen.Async`` was deprecated in Release 1.68, removed in Release 1.70. Bio.PopGen.FDist ---------------- ``Bio.PopGen.FDist`` was deprecated in Release 1.68, removed in Release 1.70. Bio.PopGen.SimCoal ------------------ ``Bio.PopGen.SimCoal`` was deprecated in Release 1.68, and removed in Release 1.70. Bio.UniGene ----------- Submodule Bio.UniGene.UniGene which was an HTML parser was declared obsolete in Release 1.59, deprecated in Release 1.61, and removed in Release 1.64. Bio.SubsMat ----------- The methods ``print_full_mat`` and ``print_mat`` were removed from the `SeqMat`` class in Bio.SubsMat in Release 1.79. The Bio.SubsMat module was deprecated in Release 1.78, and removed in Release 1.80. As an alternative, please consider using Bio.Align.substitution_matrices. Bio.Align --------- The ``infer_coordinates`` class method of the ``Alignment`` class in ``Bio.Align`` was deprecated in Release 1.84, and removed in Release 1.86. Instead, please use the ``parse_printed_alignment`` method, which is much faster, and returns both the coordinates and sequences after removing the gaps. The ``get_column`` method of the MultipleSeqAlignment was deprecated in Release 1.57 and removed in Release 1.69. The ``add_sequence`` method of the MultipleSeqAlignment was deprecated in Release 1.57 and should have been removed in Release 1.69. It was actually removed in Release 1.79. The ``format`` method of the MultipleSeqAlignment class and the PairwiseAlignment class were deprecated in Release 1.76. This decision was reversed in Release 1.79. The ``__format__`` method of the Array class in Bio.Align.substitution_matrices was deprecated in Release 1.79. The PairwiseAlignment class was deprecated in Release 1.80, and removed in Release 1.82. Please use the new Alignment class instead. Attributes of the PairwiseAligner class referring to gap scores were renamed in Release 1.86, with the original name still available with a deprecation warning. These attributes were renamed to be consistent with the AlignmentCounts class and with the common nomenclature in the literature. The default value of the gap score of a PairwiseAligner object was changed in Release 1.86. Previously, for consistency with Bio.pairwise2, the default value for gap score was 0. However, this means that a mismatch, an insertion followed by a deletion, and a deletion followed by an insertion all get assigned a score of 0. The aligner then finds a large number of alignments that are logically the same, but with trivial differences between them. For example, aligning AAACAAA to AAAGAAA previously yielded the following three alignments, all with score 6: AAACAAA AAAC-AAA AAA-CAAA AAAGAAA AAA-GAAA AAAG-AAA With the new default parameter for the gap score, only the first alignment is returned. The ``alphabet`` attribute of the PairwiseAligner class was deprecated in Release 1.86. The attribute is still being stored, but it is not used in any way. Bio.Align.Generic ----------------- This module which defined to original (Multiple-Sequence) Alignment class was deprecated in Release 1.57 and removed in Release 1.69. Bio.ParserSupport ----------------- ``Bio.ParserSupport`` was declared obsolete in Release 1.59, and deprecated in Release 1.63. The Martel specific ``EventGenerator`` was removed in Release 1.67, and the entire module was removed in Release 1.72. Bio.KDTree ---------- This module was declared obsolete in Release 1.72, deprecated in Release 1.74, and removed in Release 1.77. As of Release 1.72, KDTree data structures and the functionality previously available in ``Bio.KDTree`` are provided in a new module ``Bio.PDB.kdtrees``. Bio.trie, Bio.triefind ---------------------- These modules were declared obsolete in Release 1.72, deprecated in Release 1.73, and removed in Release 1.77. We suggest pygtrie as an alternative library implementing a trie data structure. Bio.Statistics -------------- This module was declared obsolete in Release 1.74, deprecated in Release 1.76, and removed in Release 1.79. Bio.File -------- The UndoHandle class was deprecated in Release 1.77, and moved to Bio/SearchIO/_legacy/ParserSupport.py, which was the only module in Biopython still using this class. The UndoHandle class in Bio.File was removed in Release 1.79. Bio.FSSP ----------- Deprecated in Release 1.77, and removed in Release 1.79. Bio.Phylo._utils ---------------- The ``draw_graphviz`` function was removed in Release 1.79. Bio.pairwise2 ------------- The ``Bio.pairwise2`` module was deprecated in Release 1.80. Bio.Wise -------- The ``Bio.Wise`` module was deprecated in Release 1.80, and removed in Release 1.82. Bio.Nexus --------- The ``original_taxon_order`` attribute of the ``Nexus`` class in ``Bio.Nexus.Nexus`` was deprecated in Release 1.80, and removed in Release 1.85. Please use the ``taxlabels`` attribute instead. Scripts/Restriction/ranacompiler.py ----------------------------------- The ``is_palindrom`` function was removed in Release 1.79.