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: University of Washington, CoMotion license@uw.edu and cc bge (at) uw.edu Include Phred/Phrap/Consed License in the subject line or go to the link below to download a license https://els2.comotion.uw.edu/product/phred-phrap-consed-autofinish 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 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: linux (32 bit), linux (64 bit--amd64 or EM64T), macosx-intel, macosx-ppc, solaris-sparc (which version?), solaris-intel OS: Example: OS: hpux Note: Consed is not available for PC's running Windows, XP, NT, or 2000. ID: (Consed requestors only) The number displayed when you view page http://bozeman.mbt.washington.edu/consed/find_unique_id.html on the computer you will use to download consed. (What is this number and why must you send it to me? This is a unique identifier you transmit to *any* web site you visit--you are not giving me any private information. This allows my web server to know that the request to download consed is coming from someone who has a license. Otherwise you will not be able to download consed. This number is often not the same as the real IP--you must use the http://bozeman.mbt.washington.edu/consed/find_unique_id.html to find this number. This number *never* starts with "10.") ID: Example: ID: 123.49.74.80 If you want Consed/Autofinish, you must include OS and ID (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: Brent Ewing, bge (at) u.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.