Convert a sequence file

Available formats

• ABI / AB1 trace — Sanger capillary sequencing trace (ABI/AB1). Read-only input: the base calls and their quality scores are extracted.
• ABI / AB1 trace (quality trimmed) — ABI/AB1 trace with Mott's quality trimming applied to the read ends. Read-only input.
• ACE assembly contigs — Sequence assembly file. Read-only input: contig sequences and their quality scores are extracted.
• mmCIF structure (observed residues) — mmCIF structure. Read-only input: the protein sequence is built from observed residues in the atom coordinates.
• mmCIF structure (declared sequence) — mmCIF structure. Read-only input: the full declared polymer sequence is read.
• Clustal alignment — Clustal multiple sequence alignments.
• EMBL — EMBL flat-file sequence records with features and annotations.
• EMBL coding sequences (CDS) — EMBL flat file. Read-only input: extracts CDS features as protein records, one per coding sequence.
• EMBOSS pairwise alignment — EMBOSS pairwise alignment output, for example from needle or water. Read-only input.
• FASTA — FASTA sequence records.
• FASTA (two-line) — FASTA with exactly two lines per sequence record.
• FASTA (BLAST-style comments) — FASTA that may contain comment lines starting with !, #, or ;. Read-only input.
• FASTA -m 10 alignment output — Pairwise alignments from the FASTA package's -m 10 output. Read-only input.
• FASTA (Pearson-style comments) — FASTA that may have comment lines before the first record or lines starting with ;, as in William Pearson's FASTA software. Read-only input.
• FASTQ (Sanger PHRED+33) — Sanger FASTQ records with PHRED quality scores.
• FASTQ (Illumina PHRED+64) — FASTQ records using Illumina quality scores.
• FASTQ (Solexa+64) — FASTQ records using Solexa quality scores.
• Gene Construction Kit (GCK) — Gene Construction Kit file holding one sequence. Read-only input.
• GenBank — GenBank or GenPept flat-file sequence records.
• GenBank coding sequences (CDS) — GenBank flat file. Read-only input: extracts CDS features as protein records, one per coding sequence.
• GFA 1 graph segments — Graphical Fragment Assembly version 1 graph. Read-only input: segment sequences are extracted.
• GFA 2 graph segments — Graphical Fragment Assembly version 2 graph. Read-only input: segment sequences are extracted.
• IntelliGenetics — IntelliGenetics sequence files. Read-only input.
• IMGT (EMBL variant) — IMGT variant of the EMBL flat-file format.
• MAF alignment — Multiple Alignment Format (MAF) sequence alignments.
• Mauve XMFA alignment — Mauve extended multi-FASTA (XMFA) alignments.
• MSF alignment — MSF multiple sequence alignments. Read-only input.
• NEXUS alignment — NEXUS multiple sequence alignments.
• UCSC nib — UCSC nib file holding one DNA sequence (A, C, G, T, N) without a record name.
• PDB structure (observed residues) — PDB structure. Read-only input: the protein sequence is built from observed residues in the atom coordinates.
• PDB structure (declared sequence) — PDB structure. Read-only input: the protein sequence declared in the SEQRES records is read.
• PHRED PHD — PHRED PHD base calls with per-base quality scores.
• PHYLIP alignment (interleaved) — Interleaved PHYLIP alignments with IDs of up to 10 characters.
• PHYLIP alignment (relaxed names) — PHYLIP alignments with longer IDs that contain no spaces.
• PHYLIP alignment (sequential) — Sequential PHYLIP alignments with IDs of up to 10 characters.
• PIR / NBRF — PIR / NBRF sequence records.
• QUAL quality scores — Quality scores in a FASTA-like layout, without sequence letters.
• SeqXML — Simple Sequence XML records.
• SFF flowgram reads — Standard Flowgram Format reads with quality scores and flow data.
• SFF flowgram reads (trimmed) — SFF reads with the trimming recorded in the file applied. Read-only input.
• SnapGene — SnapGene file holding one sequence with its features. Read-only input.
• Stockholm alignment — Stockholm (Pfam) multiple sequence alignments.
• Swiss-Prot / UniProt text — Swiss-Prot / UniProt flat-file protein records. Read-only input.
• Tab-separated (ID and sequence) — Two-column tab-separated records: ID, then sequence.
• UCSC twoBit — UCSC twoBit genome sequence files. Read-only input.
• UniProt XML — UniProt XML protein records. Read-only input.
• DNA Strider / Serial Cloner (xdna) — DNA Strider / Serial Cloner file holding one sequence.