If lastz is run with the target having the [multiple] sequence specification, then the rdotplot output is very jumbled and it does not appear to plot well (to be clear it seems to just completely overlap all the chromosomes in the target and query)
Edit: to be clear the command would be something like this
lastz "A.fa[multiple]" "B.fa[multiple]" --format=rdotplot > out.txt
Are there any workarounds?
The alternative GMAJ applet appears to not work with recent versions of java
(Exception in thread "main" java.lang.ClassCastException: java.lang.StringBuffer cannot be cast to java.lang.String at edu.psu.bx.gmaj.MajGui.setDefaults(MajGui.java:272) at edu.psu.bx.gmaj.Maj.<init>(Maj.java:53) at edu.psu.bx.gmaj.MajMain.main(MajMain.java:86))