codon optimize cds paired with taxids singlefastas gui DOI

Linux GUI app to codon optimize a directory with fasta files using taxonomy ids imported as a 1-column txt file (1 taxonomy id for each file)


  1. linux OS (tested on ubuntu 20.04 LTS)
  2. python 3.8.2 or later
  3. anaconda or miniconda
  4. Gooey conda install -c conda-forge gooey(if you get errors during installation or runtime try installing gtk sudo apt-get install libgtk-3-dev)
  5. biopython pip install biopython
  6. pandas pip install pandas
  7. dnachisel pip install dnachisel

linux desktop app installation

  1. open a linux text editor and edit in the python file the shebang line (to find where python is type in the terminal which python3)
  2. convert to executable with chmod +x
  3. open a linux text editor and edit the PATHs in the .desktop file
  4. move the file to /usr/share/applications
  5. reboot your machine


The output single-fasta files will have the same prefix as the input ones and as suffix the taxonomy id of the organism they are codon optimized for


View Github