• mase (Multiple Alignment Sequence Editor

    Don Faulkner and Jerzy Jurka designed and implemented an editor for genetic sequences. Mase was designed to simplify the manipulation of aligned sequence sets. It contains functionality for many of the common tasks related to this goal. In addition, mase was designed with a very modular approach, making additions or modifications to the code straightforward. The mase program was published in "Trends in Biochemical Sciences", vol. 13, pp. 321-322, 1988. You can download the Mase program and the mase browser
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    MASE: Multiple Alignment Sequence Editor

    1. Advantages:

      1. User Friendly: Menu driven Interface.

    2. Disadvantages

      1. No Boxed Output: The MASE program does not create a boxed alignment--It only outputs a textual alignment, similar to the GCG program "pretty". However, it is possible to take the data generated from the mase program and convert it to a GCG multiple sequence format so that you can use the GCG pretty program or the EGCG prettyplot/prettybox programs to produce publication quality boxed/shaded alignments. Creating a Boxed Alignment. 
    

    The following is a short tutorial on how to edit a group of
sequences with the MASE program.

    
cyrus%      tbl-to-IG horse.align > horse.mase <Return>


    cyrus% mase horse.mase <Return>

    


    
In order to use the mase program, you must have a file of aligned
sequences in IG format.  You will most likely first run a program like
pimaII to generate an alignment file, and then use the program
"tbl-to-IG" to convert the alignment to IG format.  Once you have a file
of sequences in IG format, you can edit them by typing:


    cyrus% mase peps.ig<Return>


    
Here are some notes on using mase:

    

 mase
instructions


    
For more information on using mase, use the unix "man" command:

    

    cyrus% man mase<Return>