Sequence conversion

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Alphabet: None DNA RNA Protein Nucleotide

Format About format
abi Reads the ABI "Sanger" capillary sequence traces files, including the PHRED quality scores for the base calls. This allows ABI to FASTQ conversion. Note each ABI file contains one and only one sequence (so there is no point in indexing the file).
ace Reads the contig sequences from an ACE assembly file. Uses Bio.Sequencing.Ace internally clustal The alignment format of Clustal X and Clustal W. See also the Bio.Clustalw module.
clustal The alignment format of Clustal X and Clustal W.
embl The EMBL flat file format. Uses Bio.GenBank internally.
fasta This refers to the input FASTA file format introduced for Bill Pearson's FASTA tool, where each record starts with a '>' line. Resulting sequences have a generic alphabet by default.
fastq FASTQ files are a bit like FASTA files but also include sequencing qualities. In Biopython, 'fastq' refers to Sanger style FASTQ files which encode PHRED qualities using an ASCII offset of 33. See also the incompatible 'fastq-solexa' and 'fastq-illumina' variants.
fastq-solexa FASTQ files are a bit like FASTA files but also include sequencing qualities. In Biopython, 'fastq' refers to Sanger style FASTQ files which encode PHRED qualities using an ASCII offset of 33. See also the incompatible 'fastq-solexa' and 'fastq-illumina' variants.
fastq-illumina FASTQ files are a bit like FASTA files but also include sequencing qualities. In Biopython, 'fastq' refers to Sanger style FASTQ files which encode PHRED qualities using an ASCII offset of 33. See also the incompatible 'fastq-solexa' and 'fastq-illumina' variants.
genbank The GenBank or GenPept flat file format.
ig This refers to the IntelliGenetics file format, apparently the same as the MASE alignment format.
nexus The NEXUS multiple alignment format, also known as PAUP format.
phd PHD files are output from PHRED, used by PHRAP and CONSED for input.
phylip An alignment format. Truncates names at 10 characters.
pir A FASTA like' format introduced by the National Biomedical Research Foundation (NBRF) for the Protein Information Resource (PIR) database, now part of UniProt.
seqxml Simple sequence XML file format.
sff Standard Flowgram Format (SFF) files produced by 454 sequencing.
stockholm The Stockholm alignment format is also known as PFAM format.
swiss Swiss-Prot aka UniProt format.
tab Simple two column tab separated sequence files, where each line holds a record's identifier and sequence. For example, this is used by Aligent's eArray software when saving microarray probes in a minimal tab delimited text file.
qual Qual files are a bit like FASTA files but instead of the sequence, record space separated integer sequencing values as PHRED quality scores. A matched pair of FASTA and QUAL files are often used as an alternative to a single FASTQ file.
uniprot-xml UniProt XML format, successor to the plain text Swiss-Prot format.

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