Command Line: introduction

Command Line: summary
Command Line: introduction
Command Line: basic usage
Command Line: advanced usage
Command Line: argument files

From version 2.11.3.0 Jalview processes a new set of command line arguments which allow more powerful and flexible combinations of arguments, though can also be used for very simple use cases too.

These new arguments are all accessed with a --doubledash form of command line argument (with the one exception where simply opening one or more files can be performed without any arguments other than the filenames).

The old command line arguments can still be used (see the old page on command line arguments) so existing scripts utilising them should not break.
These are now deprecated and will be removed in a future version of Jalview.

However, you cannot mix old and new style arguments, so if you use any -singledash arguments (with the exception of -help or -h), they will all be interpreted as old style arguments with the new --doubledash arguments being ignored. If you have a script that uses the old arguments without any dashes, and uses the bare-word open then these will also be interpreted as old style arguments.

Warning! If you use command line arguments without any dashes and don't use the bare-word argument open then all your arguments will be interpreted as alignment files to be opened by the new command line argument process!

To launch Jalview from the command line, see running Jalview from the command line.