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External alignment file

Lepage
I have heard that one can save an alignment as a file to be called up later and used in another program to where you can have a number of programs which use this one alignment file and therefore e.g. only need to do one initial align that can be used for a number of programs.
I have tried this and the program has ignored the inserted external alignment command file completely.

Does anyone know what the right procedure is to get this to function properly?
Parents
  • I use following it works for me. Will need to set the paths.

    Build your alignment program and use this format on the last line of your program.

    SAVE/ALIGNMENT,A1,your_program_name.aln,BOTH

    Use this format in the program you want to import the alignment into

    RECALL/ALIGNMENT,EXTERNAL,a1,your_program_name:a1

    I have heard that one can save an alignment as a file to be called up later and used in another program to where you can have a number of programs which use this one alignment file and therefore e.g. only need to do one initial align that can be used for a number of programs.
    I have tried this and the program has ignored the inserted external alignment command file completely.

    Does anyone know what the right procedure is to get this to function properly?
Reply
  • I use following it works for me. Will need to set the paths.

    Build your alignment program and use this format on the last line of your program.

    SAVE/ALIGNMENT,A1,your_program_name.aln,BOTH

    Use this format in the program you want to import the alignment into

    RECALL/ALIGNMENT,EXTERNAL,a1,your_program_name:a1

    I have heard that one can save an alignment as a file to be called up later and used in another program to where you can have a number of programs which use this one alignment file and therefore e.g. only need to do one initial align that can be used for a number of programs.
    I have tried this and the program has ignored the inserted external alignment command file completely.

    Does anyone know what the right procedure is to get this to function properly?
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