<commit_before>Format name,File Extension,Read,Write,Index,BioPython Documentation Notes,Our Notes
abi,"*.abi, *.ab1",1.58,No,N/A,"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,*.ace,1.47,No,1.52,Reads the contig sequences from an ACE assembly file. Uses Bio.Sequencing.Ace internally,
clustal,*.aln,1.43,1.43,No,The alignment format of Clustal X and Clustal W.,CLUSTAL format is recognised by the word CLUSTAL at the beginning of the file.
embl,Unspecified (*.txt),1.43,1.54,1.52,The EMBL flat file format. Uses Bio.GenBank internally.,
fasta,"*.fasta, *.fas, *.fa, *.seq, *.fsa, *.fna, *.ffn, *.faa, *.frn
",1.43,1.43,1.52,"This refers to the input FASTA file format introduced for <NAME>'s FASTA tool, where each record starts with a "">"" line. Resulting sequences have a generic alphabet by default.",There is no standard file extension for a text file containing FASTA formatted sequences. Although their is a plethora of ad-hoc file extensions. See this article for details and explanation.
fastq-sanger or fastq,"*.fq, *.fastq",1.50,1.50,1.52,"FASTQ files are a bit like FASTA files but also include sequencing qualities. In Biopython, ""fastq"" (or the alias ""fastq-sanger"") 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 used in early Solexa/Illumina pipelines, Illumina pipeline 1.8 produces Sanger FASTQ.","There is no standard file extension for a FASTQ file, but .fq and .fastq, are commonly used. There are different FASTQ formats for different sequencing technologies.  "
fastq-solexa,"*.fq, *.fastq",1.50,1.50,1.52,"FASTQ files are a bit like FASTA files but also include sequencing qualities. In Biopython, ""fastq-solexa"" refers to the original Solexa/Illumina style FASTQ files which encode Solexa qualities using an ASCII offset of 64. See also what we call the ""fastq-illumina"" format.","There is no standard file extension for a FASTQ file, but .fq and .fastq, are commonly used. There are different FASTQ formats for different sequencing technologies.  "
fastq-illumina,"*.fq, *.fastq",1.51,1.51,1.52,"FASTQ files are a bit like FASTA files but also include sequencing qualities. In Biopython, ""fastq-illumina"" refers to early Solexa/Illumina style FASTQ files (from pipeline version 1.3 to 1.7) which encode PHRED qualities using an ASCII offset of 64. For good quality reads, PHRED and Solexa scores are approximately equal, so the ""fastq-solexa"" and ""fastq-illumina"" variants are almost equivalent.","There is no standard file extension for a FASTQ file, but .fq and .fastq, are commonly used. There are different FASTQ formats for different sequencing technologies.  "
genbank or gb,"*.gbk, *.gb, *.gpff",1.43,1.48 / 1.51,1.52,"The GenBank or GenPept flat file format. Uses Bio.GenBank internally for parsing. Biopython 1.48 to 1.50 wrote basic GenBank files with only minimal annotation, while 1.51 onwards will also write the features table (see Bug 2294).",See this article.
ig,Unspecified (*.txt),1.47,No,1.52,"This refers to the IntelliGenetics file format, apparently the same as the MASE alignment format.",
imgt,Unspecified (*.txt),1.56,1.56,1.56,This refers to the IMGT variant of the EMBL plain text file format.,
nexus,"*.nxs, *.nex ",1.43,1.48,No,"The NEXUS multiple alignment format, also known as PAUP format. Uses Bio.Nexus internally.",
phd,*.phd,1.46,1.52,1.52,"PHD files are output from PHRED, used by PHRAP and CONSED for input. Uses Bio.Sequencing.Phd internally.",
phylip,*.phy or *.ph,1.43,1.43,No,An alignment format. Truncates names at 10 characters.,
pir,*.pir,1.48,No,1.52,"A ""FASTA like"" format introduced by the National Biomedical Research Foundation (NBRF) for the Protein Information Resource (PIR) database, now part of UniProt.",
seqxml,*.xml,1.58,1.58,No,Simple sequence XML file format.,
sff,*.ssf,1.54,1.54,1.54,Standard Flowgram Format (SFF) binary files produced by Roche 454 and IonTorrent/IonProton sequencing machines.,
stockholm,"*.sto, *.sth",1.43,1.43,No,The Stockholm alignment format is also known as PFAM format.,
swiss,*.sw,1.43,No,1.52,Swiss-Prot aka UniProt format. Uses Bio.SwissProt internally. See also the UniProt XML format.,
tab,*.tsv,1.48,1.48,1.52,"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,1.50,1.50,1.52,"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,*.xml,1.56,No,1.56,"UniProt XML format, successor to the plain text Swiss-Prot format.",<commit_msg>Fixed "ssf" (->"sff")<commit_after>Format name,File Extension,Read,Write,Index,BioPython Documentation Notes,Our Notes
abi,"*.abi, *.ab1",1.58,No,N/A,"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,*.ace,1.47,No,1.52,Reads the contig sequences from an ACE assembly file. Uses Bio.Sequencing.Ace internally,
clustal,*.aln,1.43,1.43,No,The alignment format of Clustal X and Clustal W.,CLUSTAL format is recognised by the word CLUSTAL at the beginning of the file.
embl,Unspecified (*.txt),1.43,1.54,1.52,The EMBL flat file format. Uses Bio.GenBank internally.,
fasta,"*.fasta, *.fas, *.fa, *.seq, *.fsa, *.fna, *.ffn, *.faa, *.frn
",1.43,1.43,1.52,"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.",There is no standard file extension for a text file containing FASTA formatted sequences. Although their is a plethora of ad-hoc file extensions. See this article for details and explanation.
fastq-sanger or fastq,"*.fq, *.fastq",1.50,1.50,1.52,"FASTQ files are a bit like FASTA files but also include sequencing qualities. In Biopython, ""fastq"" (or the alias ""fastq-sanger"") 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 used in early Solexa/Illumina pipelines, Illumina pipeline 1.8 produces Sanger FASTQ.","There is no standard file extension for a FASTQ file, but .fq and .fastq, are commonly used. There are different FASTQ formats for different sequencing technologies.  "
fastq-solexa,"*.fq, *.fastq",1.50,1.50,1.52,"FASTQ files are a bit like FASTA files but also include sequencing qualities. In Biopython, ""fastq-solexa"" refers to the original Solexa/Illumina style FASTQ files which encode Solexa qualities using an ASCII offset of 64. See also what we call the ""fastq-illumina"" format.","There is no standard file extension for a FASTQ file, but .fq and .fastq, are commonly used. There are different FASTQ formats for different sequencing technologies.  "
fastq-illumina,"*.fq, *.fastq",1.51,1.51,1.52,"FASTQ files are a bit like FASTA files but also include sequencing qualities. In Biopython, ""fastq-illumina"" refers to early Solexa/Illumina style FASTQ files (from pipeline version 1.3 to 1.7) which encode PHRED qualities using an ASCII offset of 64. For good quality reads, PHRED and Solexa scores are approximately equal, so the ""fastq-solexa"" and ""fastq-illumina"" variants are almost equivalent.","There is no standard file extension for a FASTQ file, but .fq and .fastq, are commonly used. There are different FASTQ formats for different sequencing technologies.  "
genbank or gb,"*.gbk, *.gb, *.gpff",1.43,1.48 / 1.51,1.52,"The GenBank or GenPept flat file format. Uses Bio.GenBank internally for parsing. Biopython 1.48 to 1.50 wrote basic GenBank files with only minimal annotation, while 1.51 onwards will also write the features table (see Bug 2294).",See this article.
ig,Unspecified (*.txt),1.47,No,1.52,"This refers to the IntelliGenetics file format, apparently the same as the MASE alignment format.",
imgt,Unspecified (*.txt),1.56,1.56,1.56,This refers to the IMGT variant of the EMBL plain text file format.,
nexus,"*.nxs, *.nex ",1.43,1.48,No,"The NEXUS multiple alignment format, also known as PAUP format. Uses Bio.Nexus internally.",
phd,*.phd,1.46,1.52,1.52,"PHD files are output from PHRED, used by PHRAP and CONSED for input. Uses Bio.Sequencing.Phd internally.",
phylip,*.phy or *.ph,1.43,1.43,No,An alignment format. Truncates names at 10 characters.,
pir,*.pir,1.48,No,1.52,"A ""FASTA like"" format introduced by the National Biomedical Research Foundation (NBRF) for the Protein Information Resource (PIR) database, now part of UniProt.",
seqxml,*.xml,1.58,1.58,No,Simple sequence XML file format.,
sff,*.sff,1.54,1.54,1.54,Standard Flowgram Format (SFF) binary files produced by Roche 454 and IonTorrent/IonProton sequencing machines.,
stockholm,"*.sto, *.sth",1.43,1.43,No,The Stockholm alignment format is also known as PFAM format.,
swiss,*.sw,1.43,No,1.52,Swiss-Prot aka UniProt format. Uses Bio.SwissProt internally. See also the UniProt XML format.,
tab,*.tsv,1.48,1.48,1.52,"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,1.50,1.50,1.52,"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,*.xml,1.56,No,1.56,"UniProt XML format, successor to the plain text Swiss-Prot format.",
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