Manipulating biological data

Sequences and Alignments

• Loading an alignment from a file or url
• Specifying the sequence molecular type
• Making an alignment from standard python objects
• Making a sequence collection from standard python objects
• Loading sequences using format parsers
• Sequence Collections and Alignments
• Sequence
• Protein sequences
• Annotations
• Annotations with coordinates
• Molecular types
• Alphabets

Genetic code

• Available genetic codes
• Translate DNA sequences
• Translate all six frames
• Find out how many stops in a frame
• Translate a codon
• Look up the amino acid corresponding to a single codon
• Get all the codons for one amino acid
• Get all the codons for a group of amino acids
• Converting the CodonAlphabet to codon series
• Obtaining the codons from a DnaSequence object
• Translating a DNA sequence with a terminating stop codon

Trees

• Trees