Here are 47 popular functions in Biopython:

• Seq: Represents a biological sequence, such as DNA or protein.
• SeqRecord: Represents a sequence with metadata, including ID and description.
• SeqIO: Handles reading and writing sequence files in various formats.
• AlignIO: Handles reading and writing multiple sequence alignment files in various formats.
• Bio.Alphabet: Defines sequence alphabets, such as IUPAC codes for DNA and protein.
• Bio.SeqUtils: Provides various utilities for working with sequences, such as computing molecular weight and codon usage.
• Bio.SeqIO.QualityIO: Handles reading and writing FASTQ files.
• Bio.SeqIO.PhdIO: Handles reading and writing PHD files.
• Bio.SeqIO.FastaIO: Handles reading and writing FASTA files.
• Bio.SeqIO.ClustalIO: Handles reading and writing ClustalW files.
• Bio.SeqIO.EmbossIO: Handles reading and writing EMBOSS files.
• Bio.SeqIO.GenBankIO: Handles reading and writing GenBank files.
• Bio.SeqIO.SwissIO: Handles reading and writing Swiss-Prot files.
• Bio.SeqIO.TabIO: Handles reading and writing tab-separated files.
• Bio.SeqIO.NexusIO: Handles reading and writing NEXUS files.
• Bio.SearchIO: Parses search results from various tools, such as BLAST and HMMER.
• Bio.Blast: Runs BLAST searches against various databases.
• Bio.KEGG: Provides access to the KEGG database.
• Bio.PDB: Handles reading and writing PDB files, as well as structure manipulation and analysis.
• Bio.Align: Represents a multiple sequence alignment, with associated metadata and annotations.
• Bio.Align.Applications: Wrappers for running multiple sequence alignment tools, such as ClustalW and Muscle.
• Bio.Restriction: Provides tools for simulating and analyzing DNA restriction digests.
• Bio.SeqFeature: Represents a feature or annotation on a sequence, such as a gene or a mutation.
• Bio.Graphics.GenomeDiagram: Generates graphical representations of genome sequences, with features and annotations.
• Bio.Graphics.BasicChromosome: Generates basic chromosome diagrams.
• Bio.Emboss.Applications: Wrappers for running EMBOSS tools, such as Needle and Water.
• Bio.SeqIO.Example: Provides example sequence data for testing and learning.
• Bio.AlignIO.Example: Provides example alignment data for testing and learning.
• Bio.Align.AlignInfo: Computes various summary statistics and information content for a multiple sequence alignment.
• Bio.Align.PairwiseAligner: Computes pairwise alignments between two sequences.
• Bio.Motif: Represents sequence motifs, such as transcription factor binding sites.
• Bio.Motif.PWM: Represents a position weight matrix, commonly used to represent sequence motifs.
• Bio.Alphabet.IUPAC: Defines IUPAC codes for various sequence alphabets, such as DNA and protein.
• Bio.Alphabet.Gapped: Defines a gapped sequence alphabet, used for representing alignments.
• Bio.SeqIO.AceIO: Handles reading and writing ACE files, commonly used for sequencing data.
• Bio.SeqIO.GameXMLIO: Handles reading and writing GAME XML files, used for gene annotation.
• Bio.SeqIO.LasIO: A module in Biopython that provides a parser for the PacBio LAS file format. The LAS file format is used to store PacBio long-read sequencing data, including raw signal data, basecalls, and metadata.
• Bio.SeqUtils.molecular_weight(seq) – Calculates the molecular weight of a sequence.
• Bio.Phylo.PAML.codeml() – A module for running the PAML codeml program for estimating rates of evolution and selection.
• Bio.AlignIO.parse(handle, format) – Parses multiple sequence alignments from a file.
• Bio.Alphabet.IUPAC.unambiguous_dna – Defines the unambiguous DNA alphabet.
• Bio.Seq.reverse_complement(seq) – Returns the reverse complement of a sequence.
• Bio.Seq.translate(seq) – Translates a nucleotide sequence into the corresponding amino acid sequence.
• Bio.SeqUtils.seq1(seq) – Converts a protein sequence from three-letter code to one-letter code.
• Bio.SeqIO.write(records, handle, format) – Writes a sequence record or a list of sequence records to a file.
• Bio.PDB.PDBList() – A module for downloading PDB files from the RCSB PDB server.
• Bio.Blast.NCBIWWW.qblast(program, database, sequence) – Sends a sequence to the NCBI BLAST server for homology search.