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+# DNAconvert
+Convert between different file formats containing genetic information.
+
+## Installation
+Install the latest version directly using pip (requires Python 3.8 or later):
+```
+pip install git+https://github.com/iTaxoTools/DNAconvert.git#egg=DNAconvert
+```
+
+## Executables
+Download and run the standalone executables without installing Python.</br>
+[See the latest release here.](https://github.com/iTaxoTools/DNAconvert/releases/latest)
+
+## Usage
+    usage: DNAconvert [-h] [--cmd] [--allow_empty_sequences]
+                     [--informat INFORMAT] [--outformat OUTFORMAT]
+                     [infile] [outfile]
+           DNAconvert
+
+    positional arguments:
+      infile                the input file
+      outfile               the output file
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      --cmd                 activates the command-line interface
+      --allow_empty_sequences
+                            set this to keep the empty sequences in the output
+                            file
+      --disable_automatic_renaming
+                            disables automatic renaming, may result in duplicate
+                            sequence names in Phylip and Nexus files
+      --informat INFORMAT   format of the input file
+      --outformat OUTFORMAT
+                            format of the output file
+
+### Batch processing
+
+If `infile` is a directory, all files in it will be converted. In this case `informat` and `outformat` arguments are required.
+
+Specifying names of the output files:
+* `outfile` contains a '#' character: '#' will be replaced with the base names of input files.
+* `outfile` is a directory: the output files will be written in it, with the same names as input files.
+
+## Supported formats
+* `tab`: [Internal tab format][1]
+* `tab_noheaders`: [Internal tab format][1] without headers
+* `fasta`: FASTA format
+* `relaxed_phylip`: relaxed Phylip format
+* `fasta_hapview`: FASTA format for Haplotype Viewer
+* `phylip`: Phylip format
+* `fastq`: FASTQ format
+* `fasta_gbexport`: FASTA format 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
+If format is not provided, the program can infer it from the file extension
+
+Currently recognised:
+* `.tab`, `.txt`, `.tsv`: [Internal tab format][1]
+* `.fas`, `.fasta`, `.fna`: FASTA format
+* `.rel.phy`: relaxed Phylip format
+* `.hapv.fas`: FASTA format for Haplotype Viewer
+* `.phy`: Phylip format
+* `.fastq`, `.fq`: FASTQ format
+* `.fastq.gz`, `.fq.gz`: FASTQ format compressed with Gzip
+* `.gb.fas`: FASTA format for export into Genbank repository
+* `.nex`: NEXUS format
+* `.xml`: NeXML format
+* `.gb`: Genbank flat file format
+
+Files with extension `.gz` are uncompressed automatically
+
+## Adding new formats
+[Link to documentation](docs/ADDING_FORMATS.md)
+
+[1]: docs/TAB_FORMAT.md
+
+## Options
+DNAconvert uses two parsers for NEXUS format: internal (default) and the one from python-nexus package.
+
+In the file `DNAconvert/config.json` (found in `%APPDATA%\iTaxoTools` or in `$XDG_CONFIG_HOME$/`) the key-value pair
+```
+"nexus_parser" : "(method)""
+```
+determines the parser. `(method)` is either `internal` or `python-nexus`.
+
+## Generating an executable
+Using [PyInstaller](http://www.pyinstaller.org) is recommended. You should first clone the repository and install DNAconvert with all dependencies (includes PyInstaller):
+```
+git clone https://github.com/iTaxoTools/DNAconvert.git
+cd DNAconvert
+pip install ".[dev]"
+```
+
+After the following instruction, the directory `dist` will be created (among others) and the executable will be inside it:
+```
+pyinstaller scripts/DNAconvert.spec
+```
+
+## Dependencies
+Automatically installed when using pip:
+* [python\-nexus](https://pypi.org/project/python-nexus/)
+* [dendropy](https://pypi.org/project/DendroPy/)