Is there a good alignment program?

Andrew Hobbs andrewh at
Thu Dec 9 04:49:50 EST 1993

farmerj at wrote:
:      Two of my colleagues and I are looking for a program which
: will align DNA sequences from different populations and from
: different species.  We would like to be able to align several
: (ten or more) sequences at a time.

Hi, A program I use for aligning sequences is multalin.  It is
shareware (I think - but says in documentation).  It can align up to
256 sequences and up to fairly lengthy ones, but the limit is
determined by the product of lengths and number of sequences, and of
course your computer memory.  I have used it for aligning sequences of
active sites of up to 150 enzymes at once. The results can be seen on
screen with identities highlighted in color, or printed out with or
without identities in bold.  Results can also be kept in a file and
edited in a word processor if needed.  Works great.  A quick gopher
search indicates that you could get it by ftp from

as a compacted file.

:      The program we own, an older version of PCGene, is not
: adequate for our needs.  If possible, we would like to avoid
: purchasing another big program that does a huge number of things
: that we don't need to do.  We would be happy with a stand-alone
: alignment program.

:      Can anyone point us to a freeware, shareware, or commercial
: program which might meet our needs?

:      Thanks.

: James L. Farmer

: Department of Zoology
: 571 WIDB
: Brigham Young University
: Provo, Utah 84602, USA

: (801) 378-2153 (OFFICE)
: (801) 378-7499 (FAX)


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