DNAconvert

A program to convert between different file formats containing DNA sequences. Written by V. Kharchev in the framework of the iTaxoTools project. Galaxy wrapper for DNAconvert 0.1 written in 2022/2023 by F. Fischell.

Standalone executables with graphical user interface of the newest version of ASAP for Windows and Mac are available from:

http://itaxotools.org/

https://github.com/iTaxoTools/iTaxoTools-Executables/releases

For more information, see the iTaxoTools manual available at: http://itaxotools.org/

Usage

• Specify an input file and the input file format, as well as the desired output file format.
• DNAconvert will "sanitize" sequence names by replacing special characters by underscores
• For formats that require unique sequence names, DNAconvert can automatically rename sequnces by adding consecutive numbers to the names
• An important feature of DNAconvert is the option to use tab-delimited files which allows curating sequence data sets with metadata in spreadsheet editors. Refer to the iTaxoTool manual for details.

Supported formats

• tab = tsv: [Internal tab format][1] = tab-delimited text
• tab_noheaders: [Internal tab format][1] without headers = tab-delimited text without headers
• fasta: FASTA format
• phylip: Phylip format
• relaxed_phylip: relaxed Phylip format (with no restriction on the length of sequence names)
• fasta_hapview: FASTA format with sequence names formatted for Haplotype Viewer
• fastq: FASTQ format
• fasta_gbexport: FASTA format with sequence names adjusted for export into GenBank repository
• nexus: NEXUS format
• nexml: DnaCharacterMatrix in NeXML format
• genbank: Genbank flat file format
• mold_fasta: FASTA format with sequence name matching requirements for the tool MolD *

Recognised extension

Automatic recognition of file format based on extension in file name not yet available in the Galaxy implementation.