known_issues.txt

Roadmap (Known issues/feature requests/planned work)
    -- Poor error reporting when tools crash
    
    -- GUI should save standard output on exit
    
    -- Zombie process if we kill mafft.py (typically short running, but can be long on initial alignment).
    
    -- Open tempdir in Finder/Explorer if you are keeping temporaries.
    
    -- GARLI wrapper
    
    -- FastTree wrapper
    
    -- ProbAlign wrapper
    
    -- Read data first and tweak datatype (and maybe settings) for data at hand.
    
    -- js GUI and phyloplumber
    
    -- UI for partitioned model
    
    -- refactor code to separate code from built dependencies
    
    -- star
    
    -- cobalt (NIH blast aligner, but only works on small datasets)
    
    -- input aa/dna align aa tree infer from dna
    
    -- notes to developers on web page
    
    -- output to NEXUS