[Bio-software] Command window sequence alignment software

Glenn Dunshea glenn.dunshea at gmail.com
Sun Feb 5 17:40:00 EST 2006

I am trying to open software like MUSCLE that can handle large multiple
sequence alignments from a command prompt interface. In the manual for
these programs it states to launch the program simply to double click
on the program.exe file. When I do this the command window flashes on
screen for 1 second and then dissappears. This happens on different
computers in my office that run windows2000/XP and happens with
different software that uses command prompts. Does anyone know how to
fix this problem so I can operate the program(s)? Conversely does
anyone know of programs with a more friendly user interface that can
handle alignments of 1000 - 3000 sequences (clustal based programs
cannot handle this for the region I am interested in, which has
multiple indels)?

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