Exhibit 8.1

                        [LETTERHEAD OF LATHAM & WATKINS]


                                December 13, 2002



Hyseq, Inc.
670 Alamanor Avenue
Sunnyvale, California 94085

      RE:   AGREEMENT AND PLAN OF MERGER BY AND AMONG HYSEQ, INC., VERTICAL
MERGER CORP., AND VARIAGENICS, INC. DATED AS OF NOVEMBER 9, 2002

Ladies and Gentlemen:

            We have acted as counsel to Hyseq, Inc., a Nevada corporation
("Parent"), and Vertical Merger Corp., a Delaware corporation ("Merger Sub") and
wholly-owned subsidiary of Parent, in connection with the proposed merger (the
"Merger") of Merger Sub with and into Variagenics, Inc., a Delaware corporation
(the "Company"), and immediately following the Merger, the merger of the Company
with and into Parent (the "Short Form Merger") (together with the Merger, the
"Transaction"), pursuant to an Agreement and Plan of Merger by and among Parent,
Merger Sub, and the Company dated as of November 9, 2002 (the "Merger
Agreement"). This opinion is being delivered in connection with Parent's
Registration Statement on Form S-4 relating to the proposed Transaction pursuant
to the Merger Agreement (the "Registration Statement") to which this opinion
appears as an exhibit. Capitalized terms not defined herein have the meanings
specified in the Merger Agreement.

            In rendering our opinion, we have examined and, with your consent,
are expressly relying upon (without any independent investigation or review
thereof) the truth and accuracy of the statements, covenants, representations
and warranties contained in (i) the Merger Agreement (including any Exhibits,
Annexes and Schedules thereto), (ii) the Registration Statement, (iii)
representations by Parent and Merger Sub and the Company in their respective
letters which will be delivered to us at the time of the Closing (the
"Representation Letters"), and (iv) such other documents and corporate records
as we have deemed necessary or appropriate for purposes of our opinion.

            In addition, we have assumed, with your consent, that:

            1.    Original documents (including signatures) are authentic and
            documents submitted to us as copies conform to the original
            documents;

            2.    The Transaction will be consummated in the manner
            contemplated by, and in accordance with the provisions of, the
            Merger Agreement and the Registration Statement, and the Merger
            will be effective under the laws of the State of Delaware;

            3. All statements, descriptions and representations contained in any
            of the documents referred to herein or otherwise made to us are
            true, complete and correct, and no actions have been taken or will
            be taken which are inconsistent with such statements, descriptions
            or representations or which make any such statements, descriptions
            or representations untrue, incomplete or incorrect at the Effective
            Time;

            4. Any statements made in any of the documents referred to herein
            "to the knowledge of" or similarly qualified are true, complete and
            correct and will continue to be true, complete and correct at all
            times up to and including the Effective Time, in each case without
            such qualification; and

            5. The parties have complied with and, if applicable, will continue
            to comply with, the covenants contained in the Merger Agreement and
            the Registration Statement.

            Based upon and subject to the foregoing, and subject to the
qualifications and limitations stated herein, it is our opinion that, as of the
date hereof, the information in the Registration Statement set forth under the
caption "THE MERGER - Material United States Federal Income Tax Consequences of
the Transaction," to the extent that it constitutes matters of law, summaries of
legal matters, documents or proceedings, or legal conclusions, is correct in all
material respects.

            In addition to the matters set forth above, this opinion is subject
to the exceptions, limitations and qualifications set forth below.

            1. This opinion represents our best judgment regarding the
            application of United States federal income tax laws arising under
            the Internal Revenue Code of 1986, as amended, existing judicial
            decisions, administrative regulations and published rulings and
            procedures. Our opinion is not binding upon the Internal Revenue
            Service or the courts, and there is no assurance that the Internal
            Revenue Service will not assert a contrary position. Furthermore, no
            assurance can be given that future legislative, judicial or
            administrative changes, on either a prospective or retroactive
            basis, would not adversely affect the accuracy of the conclusions
            stated herein. Nevertheless, we undertake no responsibility to
            advise you of any new developments in the application or
            interpretation of the United States federal income tax laws.

            2. No opinion is expressed as to any transaction other than the
            Transaction as described in the Merger Agreement, or to any
            transaction whatsoever, including the Transaction, if, to the extent
            relevant to our opinion, either all the transactions described in
            the Merger Agreement are not consummated in accordance with the
            terms of the Merger Agreement and without waiver or breach of any
            provisions thereof or all of the representations, warranties,
            statements and assumptions upon which we have relied are not true
            and accurate at all relevant times.

            This opinion is rendered to you in connection with Parent's filing
of the Registration Statement and is not to be used, circulated, quoted or
otherwise referred to or relied upon for any other purpose without our express
written permission. In addition, this opinion letter may not be relied upon by
or furnished to any other person, firm, corporation or entity without our prior
written consent, provided however, that Company stockholders who exchange their
Company stock for Parent stock pursuant to the Transaction may rely on this
opinion. We consent to the filing of this opinion as an exhibit to the
Registration Statement and to the reference to our firm name therein under the
captions "Material United States Federal Income Tax Consequences of the
Transaction" and "Legal Matters." In giving this consent, we do not admit that
we are within the category of persons whose consent is required under Section 7
of the Securities Act of 1933, as amended, or the rules or regulations of the
Securities and Exchange Commission promulgated thereunder.

                                       Very truly yours,




                                       /s/ Latham & Watkins