ApE is a free plasmid editor, convenient to plan a cloning experiment. The Linux version is not maintained anymore, but still runs on Ubuntu 14.4 (Mac and Windows versions are both maintained).
To run on Ubuntu, download the latest Linux version, unzip and run, using:
wget http://biologylabs.utah.edu/jorgensen/wayned/ape/Download/Linux/ApE_linux_current.zip unzip ApE_linux_current.zip cd ApE Linux tclsh8.5 AppMain.tcl
If this does not work, you may have to install tk8.5 and tcl8.5:
sudo apt-get install tk8.5 tcl8.5