path: root/licenses/phrap

ACADEMIC USER AGREEMENT

Please read the entire agreement, fill in the information in the
indicated positions (such as "NAME:"), and return the entire document
to the indicated people.  Please send the document as the message--not
as an attachment.

Phrap:  A program for assembling DNA sequence data.

Swat:  A program for searching one or more DNA or protein query sequences
against a sequence database, using (an efficient implementation of) the
Smith-Waterman-Gotoh algorithm.

Cross_Match:  A general-purpose utility based on Swat for comparing any
two sets of (long or short) DNA sequences.

Phred:  A program that reads DNA sequencer trace data, calls bases,
assigns quality values to the bases, and writes the base calls and quality
values to output files.

Consed:  A program for viewing and editing Phrap assemblies.

To receive any of these programs you will need to agree to the following
conditions. They should be taken seriously!

1) You agree to read the documentation.  We welcome feedback on any
inaccuracies.

2) You agree to report any bugs to us.  (To fix bugs, we will need
from you a dataset and a procedure that reproduces the problem; but do
not send datasets without first emailing us to describe the nature of
the bug.)

3) You agree not to make the programs (including source code,
executables, or any part thereof, in modified or unmodified form)
available to anyone outside your group, and not to put them where they
may be accessible to outside individuals without your direct knowledge
(e.g. on a computer to which people outside your group have login
privileges).  The documentation however may be freely distributed.
Refer any requests for the programs to the authors.  If you are
operating a computer facility which provides access to several
independent investigators, you agree to set the permissions on the
executables and source code to allow execute but not read access, so
that the programs may not be copied. Investigators who want copies of
the software for their own use must return a separate copy of this
agreement.

4) You agree not to use the programs for any commercial purpose,
including but not limited to commercially restricted sequencing
(defined as sequencing for which a company retains patenting or
licensing rights regarding the sequence, or the right to restrict or
delay dissemination of the sequence; with the sole exception that
sequencing is not considered to be commercially restricted if it is
federally funded and the investigators adopt the data release policies
endorsed at the Wellcome Trust-sponsored Bermuda meeting,
i.e. immediate release of data as it is generated).
 [If you wish to obtain the software for commercially restricted
sequencing or any other commercial purposes, you will need to execute
a separate licensing agreement with the University of Washington and
pay a fee. In that case please contact:

Lisa Heinz
University of Washington TechTransfer, Digital Ventures
Box 354990
4311-11th Avenue NE, Suite 500
Seattle, WA  98105-4608

http://depts.washington.edu/techtran

206-616-3451  FAX: 206-616-3322
swxfr@u.washington.edu

Do not contact her if the academic license applies.]

5) You acknowledge that the software is experimental in nature and is
supplied "AS IS", without obligation by the authors or the University
of Washington to provide accompanying services or support.  The entire
risk as to the quality and performance of the Software is with you.
UW AND THE AUTHORS EXPRESSLY DISCLAIM ANY AND ALL WARRANTIES
REGARDING THE SOFTWARE, WHETHER EXPRESS OR IMPLIED, INCLUDING BUT NOT
LIMITED TO WARRANTIES PERTAINING TO MERCHANTABILITY OR FITNESS FOR A
PARTICULAR PURPOSE.

6) All members of your group with access to the software agree to the
same conditions.



Having read the above, if you are still interested in obtaining the
programs, please return a copy of this entire message (which MUST be
included so that it is clear what you are agreeing to) by email
together with the following information:

NAME: Your name in first name/last name order.

NAME:  


Example:
NAME: John Dracula
(Please do not use all capitals such as John DRACULA)

ACKNOWLEDGEMENT: An acknowledgement that you and the members of your
group agree to these conditions.

ACKNOWLEDGEMENT:

Example:
ACKNOWLEDGEMENT: I agree to the license.

PROGRAMS: Which programs you want (phrap,cross_match, and swat are
distributed together). You must cc the message to each appropriate
individual (Brent Ewing, David Gordon, and/or Phil Green) at the email
addresses below so that they will know to send you the appropriate
program.

PROGRAMS:

Example:
PROGRAMS: phred, phrap, consed

INSTITUTION: Your academic or government institution (give full name,
not abbreviation)

INSTITUTION: 

Example:
INSTITUTION:  University of Lower Transylvania

DEPARTMENT: Your department

DEPARTMENT:

Example:
DEPARTMENT:  Department of Hematology

EMAIL: Your email address for all future correspondence. Ideally this
should be a Unix computer running a generic mail program, since
several of the programs are sent as uuencoded files which may be
corrupted by some mail programs.
  If this address is not at the institution & department listed above,
please explain the discrepancy.

EMAIL: 

Example:
EMAIL: john.dracula@utrans.edu

OS: (Consed requestors only) Which platform(s) you want Consed for:
solaris 2.5.1, solaris 2.6, solaris 2.7 (solaris 7), solaris 8,
solaris 9, digital unix 4.0 (or better), hp-ux 11.x, sgi irix 6.2,
6.3, 6.4, or 6.5, linux (normal 32 bit) (Redhat 7.1-1 or better),
linux (Itanium), linux (AMD64), ibm aix 5.2 (or better), macosx 10.2
(Darwin kernel 6.0) (or better), or solaris-intel (2.8 or better).

OS:

Example:
OS: hpux

Note: Consed is not available for PC's running Windows, XP, NT, or
2000.

IP: (Consed requestors only) The ip address of the computer on which
you will be running a web browser to download consed.  This does not
have to be the same computer as the one on which you will run consed.
Please view page
http://bozeman.mbt.washington.edu/consed/find_ip_address.html
which will tell you what my computer thinks is your ip address.

(Even if you think you know your ip address, firewalls and proxies can
cause your browser to transmit a different ip address, and thus my
webserver would deny you access to consed.  So it would be a good idea
to view the page above and send me the ip address it shows, even if
this isn't your real ip address.)

IP:

Example:
IP: 123.49.74.80


If you want Consed/Autofinish, you must include OS and IP (above).
Consed cannot be obtained without them.

Please return this entire agreement so it is clear what you are
agreeing to.

Please send all of this, including the agreement, as part of the
email message--not as an attachment.  

Send it to each of the relevant individuals below:

Contacts for obtaining the programs and for questions, bug reports,
suggestions:

      Phrap/cross_match/swat:  Phil Green, phg (at) u.washington.edu
      Phred: Brent Ewing, bge (at) u.washington.edu
      Consed: David Gordon, gordon (at) genome.washington.edu

where the " (at) " is replaced by "@".

It can take up to 2 weeks for a license application to be processed,
so please be patient.