diff --git a/doc/tutorial/structure/index.rst b/doc/tutorial/structure/index.rst
index 46a2307f4..32b550994 100644
--- a/doc/tutorial/structure/index.rst
+++ b/doc/tutorial/structure/index.rst
@@ -54,4 +54,3 @@ contains functions for structure analysis and manipulation.
     measurement
     segments
     nucleotide
-    trajectories
diff --git a/environment.yml b/environment.yml
index ba7cc77ec..8e484d75c 100644
--- a/environment.yml
+++ b/environment.yml
@@ -19,10 +19,10 @@ dependencies:
   # Biotite dependencies
   - msgpack-python >=0.5.6
   - networkx >=2.0
-  - numpy >=1.15, <2.0
+  - numpy >=2.0
   - requests >=2.12
   # Testing
-  - mdtraj >=1.9.3, <1.10
+  # - mdtraj >=1.9.3, <1.10  # tempoarily disabled due to incompatibility with numpy 2.0
   - pytest >=7.0
   # Interfaced software in biotite.application (can also be installed separately)
   - autodock-vina
diff --git a/pyproject.toml b/pyproject.toml
index f1fa2e07b..fe580be37 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -18,13 +18,10 @@ classifiers = [
     "Programming Language :: Python :: Implementation :: CPython",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
-# Based on https://github.com/scipy/oldest-supported-numpy/blob/main/setup.cfg
-# When updating our minimum supported python version follow minimums set in this setup.cfg
-# as of 2022-01 for 3.7 "numpy >= 1.14.5", for 3.8 "numpy >= 1.17.3", for 3.9 "numpy >= 1.19.3"
-# this should be manually updated as the minimum python version increases
+
 dependencies = [
   "requests >= 2.12",
-  "numpy >= 1.14.5, < 2.0",
+  "numpy >= 2.0",
   "msgpack >= 0.5.6",
   "networkx >= 2.0",
 ]
@@ -68,7 +65,7 @@ requires = [
     "hatchling",
     "hatch-vcs == 0.4",
     "hatch-cython == 0.5",
-    "oldest-supported-numpy",
+    "numpy >= 2.0",
     "cython >= 3.0",
 ]
 build-backend = "hatchling.build"
diff --git a/src/biotite/sequence/align/alignment.py b/src/biotite/sequence/align/alignment.py
index 2f824c7f0..7d97d15a8 100644
--- a/src/biotite/sequence/align/alignment.py
+++ b/src/biotite/sequence/align/alignment.py
@@ -22,7 +22,7 @@ class Alignment(object):
     An :class:`Alignment` object stores information about which symbols
     of *n* sequences are aligned to each other and it stores the
     corresponding alignment score.
-    
+
     Instead of saving a list of aligned symbols, this class saves the
     original *n* sequences, that were aligned, and a so called *trace*,
     which indicate the aligned symbols of these sequences.
@@ -31,16 +31,16 @@ class Alignment(object):
     Each element of the trace is the index in the corresponding
     sequence.
     A gap is represented by the value -1.
-    
+
     Furthermore this class provides multiple utility functions for
     conversion into strings in order to make the alignment human
     readable.
-    
+
     Unless an :class:`Alignment` object is the result of an multiple
     sequence alignment, the object will contain only two sequences.
-    
+
     All attributes of this class are publicly accessible.
-    
+
     Parameters
     ----------
     sequences : list
@@ -49,7 +49,7 @@ class Alignment(object):
         The alignment trace.
     score : int, optional
         Alignment score.
-    
+
     Attributes
     ----------
     sequences : list
@@ -58,10 +58,10 @@ class Alignment(object):
         The alignment trace.
     score : int
         Alignment score.
-    
+
     Examples
     --------
-    
+
     >>> seq1 = NucleotideSequence("CGTCAT")
     >>> seq2 = NucleotideSequence("TCATGC")
     >>> matrix = SubstitutionMatrix.std_nucleotide_matrix()
@@ -107,11 +107,11 @@ def _gapped_str(self, seq_index):
             else:
                 seq_str += "-"
         return seq_str
-    
+
     def get_gapped_sequences(self):
         """
         Get a the string representation of the gapped sequences.
-        
+
         Returns
         -------
         sequences : list of str
@@ -119,7 +119,7 @@ def get_gapped_sequences(self):
             as in `Alignment.sequences`.
         """
         return [self._gapped_str(i) for i in range(len(self.sequences))]
-    
+
     def __str__(self):
         # Check if any of the sequences
         # has an non-single letter alphabet
@@ -143,7 +143,7 @@ def __str__(self):
             return ali_str[:-2]
         else:
             return super().__str__()
-    
+
     def __getitem__(self, index):
         if isinstance(index, tuple):
             if len(index) > 2:
@@ -162,13 +162,13 @@ def __getitem__(self, index):
             )
         else:
             return Alignment(self.sequences, self.trace[index], self.score)
-    
+
     def __iter__(self):
         raise TypeError("'Alignment' object is not iterable")
-    
+
     def __len__(self):
         return len(self.trace)
-    
+
     def __eq__(self, item):
         if not isinstance(item, Alignment):
             return False
@@ -179,7 +179,7 @@ def __eq__(self, item):
         if self.score != item.score:
             return False
         return True
-    
+
     @staticmethod
     def _index_sequences(sequences, index):
         if isinstance(index, (list, tuple)) or \
@@ -193,19 +193,19 @@ def _index_sequences(sequences, index):
             raise IndexError(
                 f"Invalid alignment index type '{type(index).__name__}'"
             )
-    
+
     @staticmethod
     def trace_from_strings(seq_str_list):
         """
         Create a trace from strings that represent aligned sequences.
-        
+
         Parameters
         ----------
         seq_str_list : list of str
             The strings, where each each one represents a sequence
             (with gaps) in an alignment.
             A ``-`` is interpreted as gap.
-        
+
         Returns
         -------
         trace : ndarray, dtype=int, shape=(n,2)
@@ -238,22 +238,22 @@ def get_codes(alignment):
     Instead of the indices of the aligned symbols (trace), the return
     value contains the corresponding symbol codes for each index.
     Gaps are still represented by *-1*.
-    
+
     Parameters
     ----------
     alignment : Alignment
         The alignment to get the sequence codes for.
-    
+
     Returns
     -------
     codes : ndarray, dtype=int, shape=(n,m)
         The sequence codes for the alignment.
         The shape is *(n,m)* for *n* sequences and *m* alignment cloumn.
         The array uses *-1* values for gaps.
-    
+
     Examples
     --------
-    
+
     >>> seq1 = NucleotideSequence("CGTCAT")
     >>> seq2 = NucleotideSequence("TCATGC")
     >>> matrix = SubstitutionMatrix.std_nucleotide_matrix()
@@ -267,14 +267,17 @@ def get_codes(alignment):
     """
     trace = alignment.trace
     sequences = alignment.sequences
-    
+
     # The number of sequences is the first dimension
-    codes = np.zeros((trace.shape[1], trace.shape[0]), dtype=int)
+    codes = np.zeros((trace.shape[1], trace.shape[0]), dtype=np.int64)
     for i in range(len(sequences)):
+        # Mark -1 explicitly as int64 to avoid that the unsigned dtype
+        # of the sequence code is used
+        # (https://numpy.org/neps/nep-0050-scalar-promotion.html)
         codes[i] = np.where(
-            trace[:,i] != -1, sequences[i].code[trace[:,i]], -1
+            trace[:,i] != -1, sequences[i].code[trace[:,i]], np.int64(-1)
         )
-    
+
     return np.stack(codes)
 
 
@@ -283,24 +286,24 @@ def get_symbols(alignment):
     Similar to :func:`get_codes()`, but contains the decoded symbols
     instead of codes.
     Gaps are still represented by *None* values.
-    
+
     Parameters
     ----------
     alignment : Alignment
         The alignment to get the symbols for.
-    
+
     Returns
     -------
     symbols : list of list
         The nested list of symbols.
-    
+
     See Also
     --------
     get_codes
 
     Examples
     --------
-    
+
     >>> seq1 = NucleotideSequence("CGTCAT")
     >>> seq2 = NucleotideSequence("TCATGC")
     >>> matrix = SubstitutionMatrix.std_nucleotide_matrix()
@@ -317,8 +320,8 @@ def get_symbols(alignment):
         alphabet = alignment.sequences[i].get_alphabet()
         codes_wo_gaps = codes[i, codes[i] != -1]
         symbols_wo_gaps = alphabet.decode_multiple(codes_wo_gaps)
-        if not isinstance(symbols_wo_gaps, list):
-            symbols_wo_gaps = list(symbols_wo_gaps)
+        if isinstance(symbols_wo_gaps, np.ndarray):
+            symbols_wo_gaps = symbols_wo_gaps.tolist()
         symbols_for_seq = np.full(len(codes[i]), None, dtype=object)
         symbols_for_seq[codes[i] != -1] = symbols_wo_gaps
         symbols[i] = symbols_for_seq.tolist()
@@ -331,7 +334,7 @@ def get_sequence_identity(alignment, mode="not_terminal"):
 
     The identity is equal to the matches divided by a measure for the
     length of the alignment that depends on the `mode` parameter.
-    
+
     Parameters
     ----------
     alignment : Alignment
@@ -348,12 +351,12 @@ def get_sequence_identity(alignment, mode="not_terminal"):
               length of the shortest sequence.
 
         Default is *not_terminal*.
-    
+
     Returns
     -------
     identity : float
         The sequence identity, ranging between 0 and 1.
-    
+
     See also
     --------
     get_pairwise_sequence_identity
@@ -368,7 +371,7 @@ def get_sequence_identity(alignment, mode="not_terminal"):
         unique_symbols = np.unique(column)
         if len(unique_symbols) == 1 and unique_symbols[0] != -1:
             matches += 1
-    
+
     # Calculate length
     if mode == "all":
         length = len(alignment)
@@ -394,7 +397,7 @@ def get_pairwise_sequence_identity(alignment, mode="not_terminal"):
 
     The identity is equal to the matches divided by a measure for the
     length of the alignment that depends on the `mode` parameter.
-    
+
     Parameters
     ----------
     alignment : Alignment, length=n
@@ -411,12 +414,12 @@ def get_pairwise_sequence_identity(alignment, mode="not_terminal"):
               length of the shortest one of the two sequences.
 
         Default is *not_terminal*.
-    
+
     Returns
     -------
     identity : ndarray, dtype=float, shape=(n,n)
         The pairwise sequence identity, ranging between 0 and 1.
-    
+
     See also
     --------
     get_sequence_identity
@@ -458,7 +461,7 @@ def get_pairwise_sequence_identity(alignment, mode="not_terminal"):
                 ])
     else:
         raise ValueError(f"'{mode}' is an invalid calculation mode")
-    
+
     return matches / length
 
 
@@ -468,7 +471,7 @@ def score(alignment, matrix, gap_penalty=-10, terminal_penalty=True):
 
     If the alignment contains more than two sequences,
     all pairwise scores are counted.
-    
+
     Parameters
     ----------
     alignment : Alignment
@@ -485,7 +488,7 @@ def score(alignment, matrix, gap_penalty=-10, terminal_penalty=True):
     terminal_penalty : bool, optional
         If true, gap penalties are applied to terminal gaps.
         (Default: True)
-    
+
     Returns
     -------
     score : int
@@ -509,7 +512,7 @@ def score(alignment, matrix, gap_penalty=-10, terminal_penalty=True):
                 # Ignore gaps
                 if code_i != -1 and code_j != -1:
                     score += matrix[code_i, code_j]
-    
+
     # Sum gap penalties
     if type(gap_penalty) == int:
         gap_open = gap_penalty
@@ -598,7 +601,7 @@ def find_terminal_gaps(alignment):
     # The terminal gaps are before all sequences start and after any
     # sequence ends
     # Use exclusive stop -> -1
-    return np.max(firsts), np.min(lasts) + 1
+    return np.max(firsts).item(), np.min(lasts).item() + 1
 
 
 def remove_terminal_gaps(alignment):
diff --git a/src/biotite/sequence/align/kmertable.pyx b/src/biotite/sequence/align/kmertable.pyx
index 98cc62dee..90d7b0569 100644
--- a/src/biotite/sequence/align/kmertable.pyx
+++ b/src/biotite/sequence/align/kmertable.pyx
@@ -1352,7 +1352,8 @@ cdef class KmerTable:
 
 
     def __iter__(self):
-        return iter(self.get_kmers())
+        for kmer in self.get_kmers():
+            yield kmer.item()
 
 
     def __reversed__(self):
@@ -3394,7 +3395,7 @@ def _to_string(table):
         else:
             symbols = str(tuple(symbols))
         line = symbols + ": " + ", ".join(
-            [str(tuple(pos)) for pos in table[kmer]]
+            [str((ref_id.item(), pos.item())) for ref_id, pos in table[kmer]]
         )
         lines.append(line)
     return "\n".join(lines)
diff --git a/src/biotite/sequence/align/permutation.pyx b/src/biotite/sequence/align/permutation.pyx
index 64a84289f..9c1ab87bd 100644
--- a/src/biotite/sequence/align/permutation.pyx
+++ b/src/biotite/sequence/align/permutation.pyx
@@ -186,6 +186,9 @@ class FrequencyPermutation(Permutation):
         The minimum and maximum value, the permutated value
         (i.e. the return value of :meth:`permute()`)
         can take.
+    kmer_alphabet : KmerAlphabet
+        The *k-mer* alphabet that defines the range of possible *k-mers*
+        that should be permuted.
 
     Notes
     -----
@@ -226,11 +229,11 @@ class FrequencyPermutation(Permutation):
     >>> permutation = FrequencyPermutation.from_table(kmer_table)
     >>> order = permutation.permute(kmer_codes)
     >>> print(order)
-    [ 0 24 20 19 16 15 14 13 12 22 21 10 11  8  7 18  6  5  4  3 23  2  1  9
+    [ 0 22 18 19  1  2  3  4  5 23 20  6  7  8  9 21 10 11 12 13 24 14 15 16
      17]
     >>> kmer_codes = kmer_codes[np.argsort(order)]
     >>> print(["..."] + ["".join(kmer_alph.decode(c)) for c in kmer_codes[-10:]])
-    ['...', 'ba', 'ar', 'rr', 'da', 'ad', 'ac', 'ca', 'br', 'ra', 'ab']
+    ['...', 'rc', 'rd', 'rr', 'ac', 'ad', 'ca', 'da', 'ab', 'br', 'ra']
     """
 
     def __init__(self, kmer_alphabet, counts):
@@ -240,7 +243,9 @@ class FrequencyPermutation(Permutation):
                 f"but {len(counts)} counts were given"
             )
         # 'order' maps a permutation to a k-mer
-        order = np.argsort(counts)
+        # Stability is important to get the same k-mer subset selection
+        # on different architectures
+        order = np.argsort(counts, stable=True)
         # '_permutation_table' should perform the reverse mapping
         self._permutation_table = _invert_mapping(order)
         self._kmer_alph = kmer_alphabet
@@ -259,8 +264,11 @@ class FrequencyPermutation(Permutation):
         return self._kmer_alph
 
 
+    @staticmethod
     def from_table(kmer_table):
         """
+        from_table(kmer_table)
+
         Create a :class:`FrequencyPermutation` from the *k-mer* counts
         of a :class:`KmerTable`.
 
diff --git a/src/biotite/sequence/align/selector.pyx b/src/biotite/sequence/align/selector.pyx
index 1bf68127f..8bfff8721 100644
--- a/src/biotite/sequence/align/selector.pyx
+++ b/src/biotite/sequence/align/selector.pyx
@@ -10,10 +10,8 @@ __all__ = ["MinimizerSelector", "SyncmerSelector", "CachedSyncmerSelector",
 cimport cython
 cimport numpy as np
 
-from numbers import Integral
 import numpy as np
 from .kmeralphabet import KmerAlphabet
-from ..alphabet import AlphabetError
 
 
 ctypedef np.int64_t int64
@@ -21,7 +19,7 @@ ctypedef np.uint32_t uint32
 
 
 # Obtained from 'np.iinfo(np.int64).max'
-DEF MAX_INT_64 = 9223372036854775807
+cdef int64 MAX_INT_64 = 9223372036854775807
 
 
 class MinimizerSelector:
@@ -54,7 +52,7 @@ class MinimizerSelector:
         This standard order is often the lexicographical order, which is
         known to yield suboptimal *density* in many cases
         :footcite:`Roberts2004`.
-    
+
     Attributes
     ----------
     kmer_alphabet : KmerAlphabet
@@ -73,7 +71,7 @@ class MinimizerSelector:
 
     References
     ----------
-    
+
     .. footbibliography::
 
     Examples
@@ -122,12 +120,12 @@ class MinimizerSelector:
         self._window = window
         self._kmer_alph = kmer_alphabet
         self._permutation = permutation
-    
+
 
     @property
     def kmer_alphabet(self):
         return self._kmer_alph
-    
+
     @property
     def window(self):
         return self._window
@@ -135,7 +133,7 @@ class MinimizerSelector:
     @property
     def permutation(self):
         return self._permutation
-    
+
 
     def select(self, sequence, bint alphabet_check=True):
         """
@@ -154,7 +152,7 @@ class MinimizerSelector:
             of the sequence and the alphabet of the
             :class:`MinimizerSelector`
             is not checked to gain additional performance.
-        
+
         Returns
         -------
         minimizer_indices : ndarray, dtype=np.uint32
@@ -162,7 +160,7 @@ class MinimizerSelector:
         minimizers : ndarray, dtype=np.int64
             The *k-mers* that are the selected minimizers, returned as
             *k-mer* code.
-        
+
         Notes
         -----
         Duplicate minimizers are omitted, i.e. if two windows have the
@@ -176,7 +174,7 @@ class MinimizerSelector:
                 )
         kmers = self._kmer_alph.create_kmers(sequence.code)
         return self.select_from_kmers(kmers)
-    
+
 
     def select_from_kmers(self, kmers):
         """
@@ -191,7 +189,7 @@ class MinimizerSelector:
             minimizers in.
             The *k-mer* codes correspond to the *k-mers* encoded by the
             given `kmer_alphabet`.
-        
+
         Returns
         -------
         minimizer_indices : ndarray, dtype=np.uint32
@@ -199,7 +197,7 @@ class MinimizerSelector:
             appears.
         minimizers : ndarray, dtype=np.int64
             The corresponding *k-mers* codes of the minimizers.
-        
+
         Notes
         -----
         Duplicate minimizers are omitted, i.e. if two windows have the
@@ -267,7 +265,7 @@ class SyncmerSelector:
         *k-mer*.
         By default, the minimum position needs to be at the start of the
         *k-mer*, which is termed *open syncmer*.
-    
+
     Attributes
     ----------
     alphabet : Alphabet
@@ -276,7 +274,7 @@ class SyncmerSelector:
         The :class:`KmerAlphabet` for *k* and *s*, respectively.
     permutation : Permutation
         The permutation.
-    
+
     See also
     --------
     CachedSyncmerSelector
@@ -291,7 +289,7 @@ class SyncmerSelector:
 
     References
     ----------
-    
+
     .. footbibliography::
 
     Examples
@@ -337,7 +335,7 @@ class SyncmerSelector:
         self._alphabet = alphabet
         self._kmer_alph = KmerAlphabet(alphabet, k)
         self._smer_alph = KmerAlphabet(alphabet, s)
-        
+
         self._permutation = permutation
 
         self._offset = np.asarray(offset, dtype=np.int64)
@@ -353,7 +351,7 @@ class SyncmerSelector:
             )
         if len(np.unique(self._offset)) != len(self._offset):
             raise ValueError("Offset must contain unique values")
-    
+
 
     @property
     def alphabet(self):
@@ -362,7 +360,7 @@ class SyncmerSelector:
     @property
     def kmer_alphabet(self):
         return self._kmer_alph
-    
+
     @property
     def smer_alphabet(self):
         return self._smer_alph
@@ -370,7 +368,7 @@ class SyncmerSelector:
     @property
     def permutation(self):
         return self._permutation
-    
+
 
     def select(self, sequence, bint alphabet_check=True):
         """
@@ -389,7 +387,7 @@ class SyncmerSelector:
             of the sequence and the alphabet of the
             :class:`SyncmerSelector`
             is not checked to gain additional performance.
-        
+
         Returns
         -------
         syncmer_indices : ndarray, dtype=np.uint32
@@ -428,7 +426,7 @@ class SyncmerSelector:
         relative_min_pos = min_pos - np.arange(len(kmers))
         syncmer_pos = self._filter_syncmer_pos(relative_min_pos)
         return syncmer_pos, kmers[syncmer_pos]
-    
+
 
     def select_from_kmers(self, kmers):
         """
@@ -442,7 +440,7 @@ class SyncmerSelector:
         ----------
         kmers : ndarray, dtype=np.int64
             The *k-mer* codes to select the syncmers from.
-        
+
         Returns
         -------
         syncmer_indices : ndarray, dtype=np.uint32
@@ -459,9 +457,9 @@ class SyncmerSelector:
         :class:`Sequence` objects.
         """
         cdef int64 i
-        
+
         symbol_codes_for_each_kmer = self._kmer_alph.split(kmers)
-        
+
         cdef int64[:] min_pos = np.zeros(
             len(symbol_codes_for_each_kmer), dtype=np.int64
         )
@@ -477,10 +475,10 @@ class SyncmerSelector:
                         f"sort keys for {len(smers)} s-mers"
                     )
             min_pos[i] = np.argmin(ordering)
-        
+
         syncmer_pos = self._filter_syncmer_pos(min_pos)
         return syncmer_pos, kmers[syncmer_pos]
-    
+
 
     def _filter_syncmer_pos(self, min_pos):
         """
@@ -538,7 +536,7 @@ class CachedSyncmerSelector(SyncmerSelector):
         *k-mer*.
         By default, the minimum position needs to be at the start of the
         *k-mer*, which is termed *open syncmer*.
-    
+
     Attributes
     ----------
     alphabet : Alphabet
@@ -547,7 +545,7 @@ class CachedSyncmerSelector(SyncmerSelector):
         The :class:`KmerAlphabet` for *k* and *s*, respectively.
     permutation : Permutation
         The permutation.
-    
+
     See also
     --------
     SyncmerSelector
@@ -562,7 +560,7 @@ class CachedSyncmerSelector(SyncmerSelector):
 
     References
     ----------
-    
+
     .. footbibliography::
 
     Examples
@@ -584,7 +582,7 @@ class CachedSyncmerSelector(SyncmerSelector):
     >>> print(["".join(kmer_alph.decode(kmer)) for kmer in syncmers])
     ['GGCAA', 'AAGTG', 'AGTGA', 'GTGAC']
     """
-    
+
     def __init__(self, alphabet, k, s, permutation=None, offset=(0,)):
         super().__init__(alphabet, k, s, permutation, offset)
         # Check for all possible *k-mers*, whether they are syncmers
@@ -593,7 +591,7 @@ class CachedSyncmerSelector(SyncmerSelector):
         # Convert the index array into a boolean mask
         self._syncmer_mask = np.zeros(len(self.kmer_alphabet), dtype=bool)
         self._syncmer_mask[syncmer_indices] = True
-    
+
 
     def select(self, sequence, bint alphabet_check=True):
         """
@@ -612,7 +610,7 @@ class CachedSyncmerSelector(SyncmerSelector):
             of the sequence and the alphabet of the
             :class:`CachedSyncmerSelector`
             is not checked to gain additional performance.
-        
+
         Returns
         -------
         syncmer_indices : ndarray, dtype=np.uint32
@@ -628,7 +626,7 @@ class CachedSyncmerSelector(SyncmerSelector):
                 )
         kmers = self.kmer_alphabet.create_kmers(sequence.code)
         return self.select_from_kmers(kmers)
-    
+
 
     def select_from_kmers(self, kmers):
         """
@@ -642,7 +640,7 @@ class CachedSyncmerSelector(SyncmerSelector):
         ----------
         kmers : ndarray, dtype=np.int64
             The *k-mer* codes to select the syncmers from.
-        
+
         Returns
         -------
         syncmer_indices : ndarray, dtype=np.uint32
@@ -660,7 +658,7 @@ class MincodeSelector:
 
     Selects the :math:`1/\text{compression}` *smallest* *k-mers* from
     :class:`KmerAlphabet`. :footcite:`Edgar2021`
-    
+
     '*Small*' refers to the lexicographical order, or alternatively a
     custom order if `permutation` is given.
     The *Mincode* approach tries to reduce the number of *k-mers* from a
@@ -682,7 +680,7 @@ class MincodeSelector:
         By default, the standard order of the :class:`KmerAlphabet` is
         used.
         This standard order is often the lexicographical order.
-    
+
     Attributes
     ----------
     kmer_alphabet : KmerAlphabet
@@ -695,10 +693,10 @@ class MincodeSelector:
         All *k-mers*, that are smaller than this value are selected.
     permutation : Permutation
         The permutation.
-    
+
     References
     ----------
-    
+
     .. footbibliography::
 
     Examples
@@ -735,12 +733,12 @@ class MincodeSelector:
             permutation_offset = permutation.min
             permutation_range = permutation.max - permutation.min + 1
         self._threshold = permutation_offset + permutation_range / compression
-    
+
 
     @property
     def kmer_alphabet(self):
         return self._kmer_alph
-    
+
     @property
     def compression(self):
         return self._compression
@@ -752,7 +750,7 @@ class MincodeSelector:
     @property
     def permutation(self):
         return self._permutation
-    
+
 
     def select(self, sequence, bint alphabet_check=True):
         """
@@ -771,7 +769,7 @@ class MincodeSelector:
             of the sequence and the alphabet of the
             :class:`MincodeSelector`
             is not checked to gain additional performance.
-        
+
         Returns
         -------
         mincode_indices : ndarray, dtype=np.uint32
@@ -786,7 +784,7 @@ class MincodeSelector:
                 )
         kmers = self._kmer_alph.create_kmers(sequence.code)
         return self.select_from_kmers(kmers)
-    
+
 
     def select_from_kmers(self, kmers):
         """
@@ -800,7 +798,7 @@ class MincodeSelector:
         ----------
         kmers : ndarray, dtype=np.int64
             The *k-mer* codes to select the *Mincode k-mers* from.
-        
+
         Returns
         -------
         mincode_indices : ndarray, dtype=np.uint32
@@ -820,7 +818,7 @@ class MincodeSelector:
 
         mincode_pos = ordering < self._threshold
         return mincode_pos, kmers[mincode_pos]
-    
+
 
 @cython.boundscheck(False)
 @cython.wraparound(False)
@@ -835,7 +833,7 @@ def _minimize(int64[:] kmers, int64[:] ordering, uint32 window,
     instead of 'x - (window-1)/2' to 'x + (window-1)/2'.
     """
     cdef uint32 seq_i
-    
+
     cdef uint32 n_windows = kmers.shape[0] - (window - 1)
     # Pessimistic array allocation size
     # -> Expect that every window has a new minimizer
@@ -865,14 +863,14 @@ def _minimize(int64[:] kmers, int64[:] ordering, uint32 window,
         reverse_argcummin = reverse_argcummins[seq_i]
         forward_cummin = ordering[forward_argcummin]
         reverse_cummin = ordering[reverse_argcummin]
-        
+
         # At ties the leftmost position is taken,
         # which stems from the reverse pass
         if forward_cummin < reverse_cummin:
             combined_argcummin = forward_argcummin
         else:
             combined_argcummin = reverse_argcummin
-        
+
         # If the same minimizer position was observed before, the
         # duplicate is simply ignored, if 'include_duplicates' is false
         if include_duplicates or combined_argcummin != prev_argcummin:
@@ -899,7 +897,7 @@ cdef _chunk_wise_forward_argcummin(int64[:] values, uint32 chunk_size):
     cdef uint32 current_min_i = 0
     cdef int64 current_min, current_val
     cdef uint32[:] min_pos = np.empty(values.shape[0], dtype=np.uint32)
-    
+
     # Any actual value will be smaller than this placeholder
     current_min = MAX_INT_64
     for seq_i in range(values.shape[0]):
@@ -911,7 +909,7 @@ cdef _chunk_wise_forward_argcummin(int64[:] values, uint32 chunk_size):
             current_min_i = seq_i
             current_min = current_val
         min_pos[seq_i] = current_min_i
-    
+
     return min_pos
 
 @cython.boundscheck(False)
@@ -930,7 +928,7 @@ cdef _chunk_wise_reverse_argcummin(int64[:] values, uint32 chunk_size):
     - There are issues in selecting the leftmost argument
     - An offset is necessary to ensure alignment of chunks with forward
       pass
-    
+
     Hence, a separate 'reverse' variant of the function was implemented.
     """
     cdef uint32 seq_i
@@ -938,7 +936,7 @@ cdef _chunk_wise_reverse_argcummin(int64[:] values, uint32 chunk_size):
     cdef uint32 current_min_i = 0
     cdef int64 current_min, current_val
     cdef uint32[:] min_pos = np.empty(values.shape[0], dtype=np.uint32)
-    
+
     current_min = MAX_INT_64
     for seq_i in reversed(range(values.shape[0])):
         # The chunk beginning is a small difference to forward
@@ -952,5 +950,5 @@ cdef _chunk_wise_reverse_argcummin(int64[:] values, uint32 chunk_size):
             current_min_i = seq_i
             current_min = current_val
         min_pos[seq_i] = current_min_i
-    
+
     return min_pos
diff --git a/src/biotite/sequence/alphabet.py b/src/biotite/sequence/alphabet.py
index 2f0d409e6..4b9fe9683 100644
--- a/src/biotite/sequence/alphabet.py
+++ b/src/biotite/sequence/alphabet.py
@@ -352,7 +352,7 @@ def encode(self, symbol):
             raise AlphabetError(
                 f"Symbol {repr(symbol)} is not in the alphabet"
             )
-        return indices[0]
+        return indices[0].item()
 
     def decode(self, code, as_bytes=False):
         if code < 0 or code >= len(self._symbols):
diff --git a/src/biotite/sequence/codon.py b/src/biotite/sequence/codon.py
index 67d2ab291..fe50c791f 100644
--- a/src/biotite/sequence/codon.py
+++ b/src/biotite/sequence/codon.py
@@ -147,8 +147,9 @@ def __getitem__(self, item):
         elif isinstance(item, int):
             # Code for amino acid -> return possible codon codes
             codon_numbers = np.where(self._codons == item)[0]
-            codon_codes = tuple(CodonTable._to_codon(codon_numbers))
-            codon_codes = tuple([tuple(code) for code in codon_codes])
+            codon_codes = tuple(
+                [tuple(code.tolist()) for code in CodonTable._to_codon(codon_numbers)]
+            )
             return codon_codes
         else:
             # Code for codon as any iterable object
diff --git a/src/biotite/structure/filter.py b/src/biotite/structure/filter.py
index d32bce085..da4d34cfb 100644
--- a/src/biotite/structure/filter.py
+++ b/src/biotite/structure/filter.py
@@ -479,7 +479,7 @@ def filter_first_altloc(atoms, altloc_ids):
                 1      CB               4.000    5.000    6.000
     """
     # Filter all atoms without altloc code
-    altloc_filter = np.in1d(altloc_ids, [".", "?", " ", ""])
+    altloc_filter = np.isin(altloc_ids, [".", "?", " ", ""])
 
     # And filter all atoms for each residue with the first altloc ID
     residue_starts = get_residue_starts(atoms, add_exclusive_stop=True)
@@ -556,7 +556,7 @@ def filter_highest_occupancy_altloc(atoms, altloc_ids, occupancies):
                 1      CB               6.000    5.000    4.000
     """
     # Filter all atoms without altloc code
-    altloc_filter = np.in1d(altloc_ids, [".", "?", " ", ""])
+    altloc_filter = np.isin(altloc_ids, [".", "?", " ", ""])
 
     # And filter all atoms for each residue with the highest sum of
     # occupancies