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multiple alignments

Xiaoqiu Huang huang at stringmtu.edu
Fri Mar 18 09:24:55 EST 1994

    You may want to try a program called MAP. The C source file map.c
    is available by anonymous ftp from cs.mtu.edu under directory pub/huang.

    The MAP program computes a multiple global alignment of sequences using
    iterative pairwise method. The underlying algorithm for aligning
    two sequences computes a best overlapping alignment bewteen
    two sequences without penalizing terminal gaps. In addition,
    long internal gaps in short sequences are not heavily penalized.
    So MAP is good at producing an alignment where there are long
    terminal or internal gaps in some sequences. The MAP program is
    designed in a space-efficient manner, so long sequences can be aligned. 

    The MAP program is written in C and runs under Unix systems on
    Sun workstations and under DOS systems on PCs.
    We think that the program is portable to many machines.

    The MAP program is described in the following paper:
    Xiaoqiu Huang, "On global sequence alignment", to appear in CABIOS.

Xiaoqiu Huang
Department of Computer Science
Michigan Technological University
Houghton, MI 49931

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