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Applied Biosystems Inc. – ‘S-4/A’ on 10/15/01

On:  Monday, 10/15/01   ·   Accession #:  912057-1-535425   ·   File #:  333-64788

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  As Of                Filer                Filing    For·On·As Docs:Size              Issuer               Agent

10/15/01  Applied Biosystems Inc.           S-4/A                  6:2.1M                                   Merrill Corp/FA

Document/Exhibit                   Description                      Pages   Size 

 1: S-4/A       Pre-Effective Amendment to Registration of          HTML   2.02M 
                          Securities Issued in a                                 
                          Business-Combination Transaction                       
 2: EX-8.1      Opinion re: Tax Matters                             HTML     11K 
 3: EX-8.2      Opinion re: Tax Matters                             HTML     13K 
 4: EX-23.1     Consent of Experts or Counsel                       HTML      9K 
 5: EX-23.2     Consent of Experts or Counsel                       HTML      9K 
 6: EX-23.3     Consent of Experts or Counsel                       HTML      9K 

As filed with the Securities and Exchange Commission on October 15, 2001.

Registration No. 333-64788

SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

AMENDMENT NO. 4
TO
FORM S-4

REGISTRATION STATEMENT

UNDER

THE SECURITIES ACT OF 1933

APPLERA CORPORATION
(Exact Name of Registrant as Specified in Its Charter)

301 Merritt 7
Norwalk, Connecticut 06851-1070
(203) 840-2000
(Address, Including Zip Code, and Telephone Number, Including
Area Code, of Registrant's Principal Executive Offices)

William B. Sawch, Esq.
Senior Vice President and General Counsel
Applera Corporation
301 Merritt 7
Norwalk, Connecticut 06851-1070
(203) 840-2000
(Name, Address, Including Zip Code, and Telephone Number, Including Area Code, of Agent For Service)

Copies to:

   Approximate date of commencement of proposed sale to the public: As soon as practicable after the effective time of the merger of a wholly owned subsidiary of the registrant with Axys Pharmaceuticals, Inc., which shall occur as soon as practicable after the effective date of this registration statement and the satisfaction of all conditions to the closing of the merger.

   If the securities being registered on this form are to be offered in connection with the formation of a holding company and there is compliance with General Instruction G, check the following box. / /

   If this form is filed to register additional securities for an offering pursuant to Rule 462(b) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. / /

   If this form is a post-effective amendment filed pursuant to Rule 462(d) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. / /

CALCULATION OF REGISTRATION FEE

(1)

Represents the maximum number of shares of Applera Corporation—Celera Genomics Group Common Stock, par value $0.01 per share ("Applera—Celera stock"), including the rights associated with those shares pursuant to Applera Corporation's Stockholder Protection Rights Agreement, issuable upon consummation of the merger based upon a maximum exchange ratio of 0.1355 shares of Applera—Celera stock to be exchanged for each share of common stock, par value $.001 per share, of Axys Pharmaceuticals, Inc., that would be outstanding if all Axys Pharmaceuticals, Inc. stock options and warrants that may be exercisable prior to the merger were exercised, and all Axys Pharmaceuticals, Inc. 8% Senior Secured Convertible Notes due 2004 outstanding on June 12, 2001 were converted.

(2)

Pursuant to Rule 457(f)(1) of the Securities Act, this amount represents the maximum aggregate offering price which would be computed by using the average of the high and low prices of Axys common stock reported by the Nasdaq National Market on July 5, 2001. This amount is estimated solely for the purpose of calculating the registration fee.

(3)

Estimated solely for purposes of calculating the registration fee required by Section 6(b) of the Securities Act of 1933, as amended, and computed pursuant to Rule 457(f) and (c) under the Securities Act based on (i) $4.13, the average of the high and low sales prices for shares of Axys common stock on the Nasdaq National Market on July 5, 2001, (ii) the number of shares of Axys common stock outstanding as of the close of business on July 5, 2001, (iii) the number of shares of Axys common stock issuable upon conversion of all outstanding Axys Pharmaceuticals, Inc. 8% Senior Secured Convertible Notes due 2004, and (iv) the estimated maximum number of options to acquire shares of Axys common stock exercisable prior to the merger. The Registration Fee was previously paid with an accompanying overpayment on or about July 9, 2001.

(4)

Includes associated rights to purchase 1/1000th of a share of Applera Corporation's Series B participating junior preferred stock. Until the occurrence of prescribed events, the rights are not exercisable, are evidenced by the certificates representing Applera—Celera stock and will be transferred only with shares of Applera—Celera stock.

   The Registrant hereby amends this Registration Statement on such date or dates as may be necessary to delay its effective date until the Registrant shall file a further amendment which specifically states that this Registration Statement shall thereafter become effective in accordance with Section 8(a) of the Securities Act of 1933, as amended, or until this Registration Statement shall become effective on such date as the Securities and Exchange Commission, acting pursuant to said Section 8(a), may determine.

October 15, 2001

Dear Stockholder:

   You are cordially invited to attend our special meeting of stockholders on November 16, 2001, at 10:00 a.m., Pacific Time, at Axys' headquarters located at 180 Kimball Way, South San Francisco, California 94080.

   At the special meeting, we will ask you to vote on the merger of Axys and Applera Corporation. In the merger, you will receive shares of Applera Corporation—Celera Genomics Group Common Stock (NYSE: CRA). The exact number of shares of Applera—Celera stock that you will receive will be determined by an exchange ratio that will be calculated based on the average closing price of Applera—Celera stock over the 10 trading days immediately preceding (but excluding) the second trading day prior to the closing of the merger as described in the accompanying proxy statement/prospectus. For each of your shares of Axys common stock, you will receive no less than 0.0813 share of Applera—Celera stock and no more than 0.1355 share of Applera—Celera stock. The merger has been structured to be tax-free to you for United States federal income tax purposes, except for cash received in place of fractional shares.

   If the merger had closed on October 1, 2001, for each of your shares of Axys common stock you would have received 0.1355 share of Applera—Celera stock having a market value of $3.25 based on the closing price of $24.00 per share of Applera—Celera stock on October 1, 2001. At the time of the special meeting, you will not necessarily know the exact number of shares or the exact market price of the Applera—Celera stock that will be issued in connection with the merger. The maximum number of shares of Applera—Celera stock that could be issued in exchange for shares of Axys common stock under the merger agreement is a total of 6,563,414 shares of Applera—Celera stock, based upon the maximum exchange ratio of 0.1355 and the number of shares of Axys common stock outstanding on the date the merger agreement was signed and the number of shares of Axys common stock issuable upon exercise of stock options, warrants and convertible notes that may be exercisable prior to the merger. We urge you to obtain current market quotations for Applera—Celera stock and Axys common stock prior to making any decision with respect to the merger.

   Applera conducts its business through two operating groups: the Celera Genomics group and the Applied Biosystems group. The Applied Biosystems group and the Celera Genomics group are not separate legal entities, and holders of these stocks are stockholders of a single company, Applera. Applera—Celera stock is a "tracking stock" which is issued by Applera and is intended to reflect the relative performance of the Celera Genomics group. Holders of Applera—Celera stock will be stockholders of Applera only and will not have an ownership interest in the Celera Genomics group. As a result, holders of Applera—Celera stock will be subject to the risks associated with an investment in Applera and all of its businesses, assets and liabilities. Applera—Celera stock is redeemable and convertible at Applera's option as described in this proxy statement/prospectus.

   We cannot complete the merger unless holders of a majority of the outstanding shares of Axys common stock vote for the approval and adoption of the merger agreement. Only stockholders who hold shares of Axys common stock at the close of business on October 1, 2001 will be entitled to vote at the special meeting.

   The enclosed proxy statement/prospectus gives you detailed information about the proposed merger and includes the merger agreement as an annex. We encourage you to read carefully the proxy statement/prospectus, including its annexes. You should also consider the matters discussed under "Risk Factors" on page 20 of the accompanying proxy statement/prospectus before voting.

   After careful consideration, the Axys board of directors has unanimously approved the merger agreement, has unanimously determined that the merger agreement and merger are advisable and fair to you and in your best interests and unanimously recommends that you vote "FOR" the approval and adoption of the merger agreement and the approval of the merger.

   Your vote is very important. Whether or not you plan to attend the special meeting, please complete, sign and date the enclosed proxy card and return it in the enclosed prepaid envelope. If you attend the special meeting, you may revoke your proxy and vote in person if you wish, even if you have previously returned your proxy card. Your prompt cooperation will be greatly appreciated.

Sincerely,



Paul J. Hastings
President and Chief Executive Officer

   This proxy statement/prospectus is dated October 15, 2001, and is first being mailed to the stockholders of Axys Pharmaceuticals, Inc. on or about October 16, 2001.

AXYS PHARMACEUTICALS, INC.

NOTICE OF SPECIAL MEETING OF STOCKHOLDERS
TO BE HELD ON NOVEMBER 16, 2001

    A special meeting of stockholders of Axys Pharmaceuticals, Inc. will be held at Axys' headquarters located at 180 Kimball Way, South San Francisco, California 94080 on November 16, 2001 at 10:00 a.m. Pacific Time, to consider and vote on the following matters described in the accompanying proxy statement/prospectus:

1.

A proposal to approve and adopt an Agreement and Plan of Merger, dated as of June 12, 2001, among Axys, Applera Corporation and Angel Acquisition Sub, Inc., a subsidiary of Applera Corporation, and to approve the merger contemplated by that agreement; and



2.

Such other and further business as may properly come before the special meeting or before any adjournment or postponement of the special meeting.

    The board of directors of Axys has fixed the close of business on October 1, 2001 as the record date for the determination of stockholders entitled to receive notice of and to vote at the special meeting. A list of the stockholders entitled to vote will be open to the examination of stockholders at the offices of Axys at 180 Kimball Way, South San Francisco, California 94080, during ordinary business hours for 10 days prior to the date of the meeting.

    Axys cannot complete the merger unless the holders of a majority of the outstanding shares of Axys common stock vote to adopt the merger agreement. Holders of Axys common stock will not have appraisal rights under Delaware law in connection with the merger.

    The board of directors of Axys has unanimously approved the merger agreement and the merger and recommends that you vote FOR approval and adoption of the merger agreement and approval of the merger. The proposal is described in more detail in the accompanying proxy statement/prospectus, which you should read in its entirety before voting. A copy of the merger agreement is attached as Annex A to the accompanying proxy statement/prospectus.

By Order of the Board of Directors,



Paul Hastings
President and Chief Executive Officer

South San Francisco, California
October 15, 2001

Your Vote Is Important!

    To be sure your shares are represented at the meeting, please complete, date, sign and return your proxy card in the enclosed postage-paid envelope as soon as possible. You may vote in person at the meeting even if you send in your proxy card.

REFERENCE TO ADDITIONAL INFORMATION

    This proxy statement/prospectus "incorporates by reference" important business and financial information about Applera that is not included or delivered with this proxy statement/prospectus. You may obtain documents incorporated by reference in this proxy statement/prospectus without charge by requesting them in writing or by telephone from Applera at the following address:

Applera Corporation
301 Merritt 7
Norwalk, Connecticut 06851-1070
(203) 840-2000
Attn.: Secretary

    If you would like to request any documents, please do so by November 9, 2001 in order to receive them before the special meeting.

    For a more detailed description of the information incorporated by reference by Applera into this proxy statement/prospectus and how you may obtain it, see "Where You Can Find More Information" on page 144.

TABLE OF CONTENTS

i

ANNEXES

Annex A  Agreement and Plan of Merger

Annex B  Opinion of JPMorgan H&Q

ii

QUESTIONS AND ANSWERS ABOUT THE MERGER

1

2

3

4

SUMMARY OF THE PROXY STATEMENT/PROSPECTUS

    We are sending this proxy statement/prospectus to holders of Axys common stock. This summary highlights selected information from this proxy statement/prospectus and may not contain all the information that is important to you. To better understand the merger, you should read this entire document carefully, including the agreement and plan of merger attached as Annex A, the opinion of JPMorgan H&Q, a division of J.P. Morgan Securities, Inc., attached as Annex B, and the other documents to which we refer. In addition, we incorporate by reference in this proxy statement/prospectus important business and financial information about Applera. You may obtain the information incorporated by reference in this proxy statement/prospectus without charge by following the instructions in the section entitled "Where You Can Find More Information" on page 144. We have included page references parenthetically to direct you to a more complete description of the topics presented in this summary.

The Companies

APPLERA CORPORATION (see page 114)
301 Merritt 7
Norwalk, Connecticut 06851-1070
(203) 840-2000

    Applera Corporation was incorporated in Delaware in 1998 and succeeded by recapitalization to the business of PE Corporation (NY) (formerly The Perkin-Elmer Corporation) in May 1999. Applera conducts its business through two operating groups: the Celera Genomics group and the Applied Biosystems group. Applera has two classes of common stock, Applera—Celera stock and Applera—Applied Biosystems stock, that are intended to reflect the relative performance of these groups. For more information about Applera's two classes of common stock, see "Description of the Applera Capital Stock" and "Risk Factors—Risks Related to a Capital Structure with Two Separate Classes of Common Stock" in this proxy statement/prospectus.

    The Celera Genomics group is engaged principally in integrating advanced technologies to create therapeutic discovery and development capabilities for internal use and for its customers and collaborators. The Celera Genomics group's businesses are its online information business and its therapeutics discovery business. The online information business is a leading provider of information based on the human genome and related biological and medical information. Pharmaceutical, biotechnology, and academic customers use this information, along with customized information technology solutions provided by the Celera Genomics group, to enhance their capabilities in the fields of life science research and pharmaceutical and diagnostic discovery and development. The Celera Genomics group recently expanded its focus to include therapeutic discovery and development. The Celera Genomics group intends to leverage its capabilities in the study of genes and proteins and their relationship to diseases, both in internal programs and through collaborations, to identify drug targets and diagnostic markers, and to discover and develop novel therapeutic candidates. Initially, the Celera Genomics group intends to focus its therapeutic discovery efforts in the field of oncology.

    The Applied Biosystems group is a world leader in the development, manufacture, sale and service of instrument systems and associated consumable products for life science research and related applications. Its products are used in various applications including the synthesis, amplification, purification, isolation, analysis and sequencing of nucleic acids, proteins and other biological molecules.

    Applera has formed Celera Diagnostics as a joint venture between the Celera Genomics group and the Applied Biosystems group in the field of diagnostics. Applera expects that Celera Diagnostics will be focused on the discovery, development, and commercialization of novel diagnostic tests.

5

    The information contained on Applera's website is not incorporated by reference in this proxy statement/prospectus.

AXYS PHARMACEUTICALS, INC. (see page 80)
180 Kimball Way
South San Francisco, California 94080
(650) 829-1000

    Axys, a Delaware corporation, is an integrated drug discovery and development company that has a broad pipeline of product candidates for chronic therapeutic applications that are partnered with world-class pharmaceutical companies, or for which Axys is seeking partners, and a portfolio of proprietary cancer related therapeutic products. Axys also has investments in affiliated businesses that use the Axys technologies. Currently, these companies include Discovery Partners International, Inc. (Nasdaq: DPII), a chemistry services company, DNA Sciences, Inc., a genetics company and Akkadix Corporation, an agricultural biotechnology company.

    The information contained on Axys' website is not incorporated by reference in this proxy statement/prospectus.

ANGEL ACQUISITION SUB, INC. (see page 114)
c/o Applera Corporation
301 Merritt 7
Norwalk, Connecticut 06851-1070
(203) 840-2000

    Angel Acquisition, a Delaware corporation, is a wholly owned subsidiary of Applera that was organized solely for purposes of completing the merger.

The Special Meeting (see page 39)

    The special meeting of stockholders of Axys will be held at 10:00 a.m. Pacific Time, on November 16, 2001, at Axys' headquarters located at 180 Kimball Way, South San Francisco, California 94080.

    At the special meeting, we will ask the holders of shares of Axys common stock to:

•

approve and adopt the merger agreement and approve the merger; and



•

conduct any other business properly brought before the meeting.

Record Date; Vote Required (see page 39)

    You can vote, or submit a proxy to vote, at the special meeting if you were a record holder of Axys common stock at the close of business on October 1, 2001, the record date for determining which holders of Axys common stock are entitled to vote at the special meeting. At the record date, there were 40,486,750 shares of Axys common stock entitled to vote at the special meeting.

    Holders of Axys common stock as of the record date are entitled to one vote per share on each matter to be voted on at the special meeting.

    The merger will be approved only if the holders of a majority of the outstanding shares of Axys common stock entitled to vote at the special meeting vote for the proposal to approve and adopt the merger agreement and approve the merger.

6

Reasons of Axys for the Merger (see page 46)

    Since its inception, Axys has been focused on developing a state-of-the-art drug discovery system. Axys believes that the effectiveness of this system has been demonstrated in its partnerships with Merck, Bayer and Aventis. To more fully take advantage of the potential of its technologies as well as the expertise of Axys' scientific teams, Axys has determined that it needs a source of new targets for drug therapies. The delivery of potential targets for drug discovery has been at the core of the work of the Celera Genomics group in the human genome, and remains so in its future plans. Hence, Axys believes that Axys and the Celera Genomics group have complementary strengths which are expected to enable the combined company to move forward more quickly and effectively in the research and development of innovative drug candidates. In addition, holders of Axys common stock will have the opportunity to participate in a larger and better capitalized organization and to benefit from potential appreciation in Applera—Celera stock. Axys believes that these and other factors should provide a greater opportunity for increased value for the stockholders of Axys than could be achieved on a stand-alone basis.

Reasons of Applera for the Merger (see page 49)

    Applera believes that the merger will enable the combined company to compete more effectively and achieve a number of strategic objectives, particularly the expansion of the business of the Celera Genomics group into therapeutic drug discovery and development. In addition, Applera believes that the culture and employees of Axys and the Celera Genomics group, as well as their respective capabilities, technology, programs and products, will be both complementary and compatible, which will facilitate integration of Axys with the Celera Genomics group.

Recommendation of the Axys Board of Directors (see page 49)

    The Axys board of directors has unanimously approved the merger agreement and the merger and has determined that the merger agreement and merger are advisable and fair to, and in the best interests of, Axys and its stockholders. The board of directors of Axys unanimously recommends that holders of Axys common stock vote FOR the approval and adoption of the merger agreement and the approval of the merger.

Opinion of Financial Advisor to the Axys Board of Directors (see page 49)

    The board of directors of Axys received an opinion dated as of June 12, 2001 from its financial advisor, JPMorgan H&Q, a division of J.P. Morgan Securities Inc., that, as of the date of the opinion and subject to the assumptions and limitations in the opinion, the "exchange ratio" specified in the merger agreement was fair, from a financial point of view, to the holders of Axys common stock. The opinion of JPMorgan H&Q is necessarily based on economic, market and other conditions as in effect on, and the information made available to it as of June 12, 2001. Some of the financial analyses performed by JPMorgan H&Q in connection with providing its opinion include calculations based on the market prices of Applera—Celera stock and Axys common stock on specified dates or during specified periods. JPMorgan H&Q was aware that the market prices of both Applera—Celera stock and Axys common stock could fluctuate in the future due to changes in market conditions or other reasons. On June 12, 2001 the last full trading day prior to the announcement of the merger agreement, the closing price of Applera—Celera stock was $41.75 per share and the closing price of Axys common stock was $3.45 per share. On October 12, 2001 the last full trading day before the date of this proxy statement/prospectus, the closing price of Applera—Celera stock was $26.80 per share and the closing price of Axys common stock was $3.54 per share. It should be understood that subsequent developments may affect this opinion and that JPMorgan H&Q does not have any obligation to update, revise, or reaffirm this opinion.

7

    This opinion is attached as Annex B to this proxy statement/prospectus. We encourage you to read this opinion in its entirety.

Terms of the Merger Agreement

    We have attached the merger agreement, which is the legal document that governs and sets the terms of the merger, as Annex A to this proxy statement/prospectus. We encourage you to read the merger agreement in its entirety.

Conversion of Shares and Options (see page 56)

    In the merger, each share of Axys common stock will be converted into the right to receive a fraction of a share of Applera—Celera stock as determined in accordance with the merger agreement and as described in this proxy statement/prospectus. The exact number of shares of Applera—Celera stock will be determined by an exchange ratio that will be calculated based on the average closing price of Applera—Celera stock over the 10 trading days immediately preceding (but excluding) the second trading day prior to the closing of the merger as follows:

•

if this 10-day average closing price is greater than $60.27, the fraction will be fixed at 0.0813 share;



•

if this 10-day average closing price is greater than $48.23 and less than or equal to $60.27, the fraction will be $4.90 divided by this 10-day average closing price;



•

if this 10-day average closing price is equal to or greater than $45.77 and less than or equal to $48.23, the fraction will be 0.1016 share;



•

if this 10-day average closing price is less than $45.77 and greater than or equal to $34.32, the fraction will be $4.65 divided by this 10-day average closing price; and



•

if this 10-day average closing price is less than $34.32, the fraction will be fixed at 0.1355 share.

    Holders will receive only whole shares of Applera—Celera stock, and will receive cash instead of fractional shares, as described in this proxy statement/prospectus under "The Merger—Fractional Shares."

Conditions to the Completion of the Merger (see page 67)

    Several conditions must be satisfied or waived before the merger will be completed. These include:

•

the approval of the merger and approval and adoption of the merger agreement by the Axys stockholders;



•

the absence of any injunction, temporary restraining order, or other legal restraint that prohibits the merger;



•

the absence of any suit or other proceeding by any government entity which seeks to prohibit the merger, limit Applera's ownership or operation of any material portion of Axys, or impose limitations on the ability of Applera to exercise ownership rights of any shares of Axys as the surviving corporation after the merger;



•

the accuracy, in all material respects, of the representations and warranties of Applera and Axys in the merger agreement;



•

the fulfillment of the obligations of Axys, Applera and Angel Acquisition under the merger agreement; and

8

•

receipt of legal opinions from counsel to the effect that the merger will qualify as a tax-free reorganization under Section 368(a) of the Internal Revenue Code of 1986, as amended.

Non-Solicitation Covenant (see page 65)

    Axys has agreed, subject to limited exceptions, not to initiate or engage in discussions with another party about a business combination with the other party prior to the termination of the merger agreement.

Termination (see page 68)

    Applera and Axys may mutually agree to terminate the merger agreement at any time. In addition, either Applera or Axys may terminate the merger agreement if specified events do or do not occur. These include:

•

if a court or government regulator permanently prohibits the merger;



•

if the merger is not completed on or before December 31, 2001, other than as a result of the failure by the party proposing to terminate the merger agreement to perform its obligations;



•

if the holders of Axys common stock fail to approve and adopt the merger agreement and approve the merger at the special meeting; or



•

if the other party breaches its representations or agreements so that a closing condition would not be satisfied and the breach, if curable, remains uncured 30 days following notice to the breaching party.

    Applera may also terminate the merger agreement if:

•

the Axys board of directors withdraws or modifies, in a manner adverse to Applera, its recommendation of the merger agreement and the merger, or approves or recommends another acquisition proposal; or



•

the Axys board of directors fails to recommend rejection of any tender offer or exchange offer for more than 15% of the outstanding shares of Axys common stock.

    The merger agreement may also be terminated by Axys if the Axys board of directors concludes in good faith after consultation with outside legal counsel that in order to avoid violating its fiduciary duties in connection with a proposal for an alternative transaction that meets specified standards, it must withdraw or modify its recommendation of the merger agreement and the merger and it withdraws or modifies its recommendation. For more information with respect to Axys' ability to terminate the merger agreement because of the fiduciary duties of its board of directors, see "The Merger—Termination of the Merger Agreement" in this proxy statement/prospectus.

Termination Fee (see page 69)

    Axys will pay Applera a fee of $5.6 million and up to $900,000 in out-of-pocket expenses if the merger agreement is terminated under circumstances including a withdrawal of or change in the recommendation of the Axys board of directors in a manner that is adverse to Applera or the completion of an alternative transaction that was publicly announced prior to the termination of the merger agreement. These circumstances are described in detail in "The Merger—Termination of the Merger Agreement—Termination Fee" in this proxy statement/prospectus.

Regulatory Matters (see page 68)

    The merger is subject to the requirements of the Hart-Scott-Rodino Act. On June 29, 2001, Applera and Axys filed the requisite Pre-Merger Notification and Report Forms with the United States

9

Federal Trade Commission and the United States Department of Justice. The waiting period under the Hart-Scott-Rodino Act expired on July 30, 2001.

Accounting Treatment (see page 73)

    For accounting and financial reporting purposes, the merger will be treated as a purchase by Applera under generally accepted accounting principles.

NYSE Listing (see page 68)

    Applera will list the Applera—Celera stock to be issued in the merger on the New York Stock Exchange.

Material United States Federal Income Tax Consequences (see page 71)

    Applera has received an opinion from Simpson Thacher & Bartlett and Axys has received an opinion from Latham & Watkins to the effect that, if the merger is completed as contemplated, the merger will qualify as a tax-free reorganization for United States federal income tax purposes, and that holders of Axys common stock will not recognize any gain or loss for United States federal income tax purposes on the exchange of their common stock for Applera—Celera stock, except to the extent they receive cash in lieu of fractional shares. These opinions are subject to certain assumptions and qualifications, as described under "The Merger—Material United States Federal Income Tax Consequences."

    Tax matters can be complicated, and the tax consequences of the merger to you will depend on your particular tax situation. You should consult your own tax advisor to fully understand the tax consequences of the merger to you.

Interests of Axys' Officers and Directors in the Merger (see page 73)

    When considering the recommendation of the Axys board of directors, you should be aware that Axys officers and directors have interests in the merger that may be different from, or in addition to, your interests as stockholders. These interests exist in part because of rights they may have under Axys employment agreements and benefits plans. In addition, the merger agreement requires that after completion of the merger Applera must cause Axys, as the company surviving the merger, to indemnify the directors and officers of Axys for events occurring before the merger, including events that are related to the merger.

Dissenters' Rights (see page 78)

    Under Delaware law, stockholders of Axys will not be entitled to exercise dissenters' appraisal rights in connection with the merger.

Comparison of Rights of Holders of Applera—Celera Stock and Axys Common Stock (see page 141)

    Applera's certificate of incorporation and bylaws and Axys' certificate of incorporation and bylaws are different. In particular, Applera—Celera stock is a "tracking stock" and Axys common stock is not. As a result, the holders of Axys common stock will have different rights as holders of Applera—Celera stock, since holders of a "tracking stock" do not have the same rights as typical common stockholders of a corporation without "tracking stock." Applera conducts its business through two operating groups: the Celera Genomics group and the Applied Biosystems group. The Applied Biosystems group and the Celera Genomics group are not separate legal entities, and holders of these stocks are stockholders of a single company, Applera. This means that the assets Applera attributes to one group could be subject to the liabilities of the other group. Holders of Applera—Celera stock will be subject to all of the risks

10

relating to an investment in Applera, including the Applied Biosystems group. Axys is a separate legal entity and holders of its common stock are subject to the benefits and risks associated with its consolidated businesses, assets and liabilities. This is not the only difference between the rights of Applera—Celera stock and Axys common stock. For more information, see "Description of Applera Capital Stock" and "Risk Factors—Risks Related to a Capital Structure with Two Separate Classes of Common Stock" in this proxy statement/prospectus.

Comparative Market Price and Dividend Information (see page 18)

    Shares of Applera—Celera stock are listed on the New York Stock Exchange under the symbol "CRA." On June 12, 2001, the last full trading day prior to the public announcement of the proposed merger, Applera—Celera stock closed at $41.75 per share. On October 12, 2001, the last full trading day prior to the date of this proxy statement/prospectus, Applera—Celera stock closed at $26.80 per share.

    Shares of Axys common stock are traded on the Nasdaq National Market under the symbol "AXPH." On June 12, 2001, the last full trading day prior to the public announcement of the proposed merger, Axys' common stock closed at $3.45 per share. On October 12, 2001, the last full trading day prior to the date of this proxy statement/prospectus, Axys' common stock closed at $3.54 per share.

11

SELECTED HISTORICAL CONSOLIDATING FINANCIAL INFORMATION AND SELECTED UNAUDITED PRO FORMA CONSOLIDATING FINANCIAL INFORMATION

    Applera Selected Historical Consolidating Financial Information

    The following selected consolidating financial information has been derived from the consolidated financial statements of Applera, the combined financial statements of the Applied Biosystems group and the combined financial statements of the Celera Genomics group for each of the five fiscal years in the period ended June 30, 2001. The information set forth below should be read in conjunction with the Applera consolidated statements, the Applied Biosystems group combined financial statements, and the Celera Genomics group combined financial statements, and related notes thereto contained in the Applera Annual Report to Stockholders for the year ended June 30, 2001, incorporated herein by reference.

    On May 6, 1999, Applera recapitalized and issued two new classes of common stock, the Applera—Celera stock and the Applera—Applied Biosystems stock, to the stockholders of Applera's predecessor. Effective November 30, 2000, Applera, which was named "PE Corporation" at the time of the recapitalization, was renamed "Applera Corporation" and the Applied Biosystems group, which was named the "PE Biosystems" group at the time of the recapitalization, was renamed the "Applied Biosystems" group. Therefore, neither the Applera—Celera stock nor the Applera—Applied Biosystems stock was issued or outstanding at any time prior to May 6, 1999.

    All share and per share amounts have been restated to reflect all prior stock splits of Applera—Applied Biosystems stock and Applera—Celera stock.

    A number of items impact the comparability of this information. Before-tax amounts include:

Applied Biosystems Group

•

Restructuring, other merger costs, and acquisition-related costs of $48.1 million for fiscal 1998, $6.1 million for fiscal 1999, and $2.1 million for fiscal 2000;



•

A restructuring reserve adjustment of $9.2 million for fiscal 1999 relating to excess fiscal 1998 restructuring liabilities;



•

Gains on investments of $64.9 million for fiscal 1997, $1.6 million for fiscal 1998, $6.1 million for fiscal 1999, $48.6 million for fiscal 2000, and $15.0 million for fiscal 2001;



•

Acquired research and development charges of $28.9 million for fiscal 1998;



•

Charges for the impairment of assets of $0.7 million for fiscal 1997 and $14.5 million for fiscal 1999;



•

Tax benefit and valuation allowance reductions of $22.2 million for fiscal 1999;



•

A charge of $3.5 million for a donation to Applera's charitable foundation for fiscal 1999;



•

Foreign currency hedge contract-related gain of $2.3 million for fiscal 1999;



•

Charges of $4.6 million for fiscal 1999 relating to the recapitalization of Applera;



•

Charges relating to the acceleration of some of Applera's long-term compensation programs as a result of the attainment of performance targets of $9.1 million for fiscal 1999 and $45.0 million for fiscal 2000; and



•

A gain of $8.2 million on the sale of real estate for fiscal 2000.

12

Celera Genomics Group

•

Acquired research and development charges of $26.8 million for fiscal 1997;



•

Charges of $5.6 million relating to the recapitalization and transformation of the Company for fiscal 1999;



•

A charge for the impairment of goodwill and other intangibles of $69.1 million for fiscal 2001; and



•

A loss of $5.0 million from the Celera Genomics group's interest in Celera Diagnostics for fiscal 2001.

13

Selected Unaudited Pro Forma Consolidating Financial Information of Applera

    The following selected unaudited pro forma consolidating financial information is derived from unaudited Applera pro forma financial statements and the notes thereto, which are included elsewhere in this proxy statement/prospectus and should be read in conjunction with those statements and related notes. See "Unaudited Pro Forma Consolidated and Consolidating Financial Statements" in this proxy statement/prospectus.

    The unaudited Applera pro forma consolidated balance sheets assume that the merger took place on June 30, 2001 and combines Applera's June 30, 2001 audited consolidated balance sheet with Axys' June 30, 2001 unaudited balance sheet. The unaudited pro forma consolidated statement of operations for the year ended June 30, 2001 gives effect to the merger as if it occurred on July 1, 2000. Because Applera and Axys have two different fiscal years, and the combined company will adopt the fiscal year of Applera, pro forma operating results are presented on a June 30 fiscal year basis.

    The unaudited pro forma consolidating financial information is presented for illustrative purposes only and is not necessarily indicative of the consolidated financial position or results of operations of future periods or the results that actually would have been realized had the entities been a single entity during this period.

Applera Corporation
Selected Unaudited Pro Forma Consolidating Financial Information
Fiscal Year Ended June 30, 2001

14

SELECTED HISTORICAL CONSOLIDATED FINANCIAL INFORMATION OF AXYS

    The following selected consolidated financial information has been derived from the consolidated financial statements of Axys (and its predecessor company) for each of the five fiscal years in the period ended December 31, 2000, and the six month periods ended June 30, 2000 and 2001. The operating results for the six months ended June 30, 2001 are not necessarily indicative of the results that may be expected for the entire fiscal year. The information set forth below should be read in conjunction with the Axys audited financial statements and notes thereto which are included in this proxy statement/prospectus commencing on page F-1, and "Axys Management's Discussion and Analysis of Financial Condition and Result of Operations" commencing on page 95 of this proxy statement/prospectus.

(1)

Reclassified results of operations in accordance with Accounting Principles Board Opinion No. 30, "Reporting the Results of Operations—Reporting the Effects of Disposal of a Segment of a Business, and Extraordinary, Unusual and Infrequently Occurring Events and Transactions" in connection with the sale of Axys Advanced Technologies and PPGx, Inc. during 2000.

(2)

Includes the results of operations of Sequana Therapeutics, Inc. from January 8, 1998 through December 31, 1998, including a one-time charge for acquired in-process research and development. Excluding this one-time charge, net loss and net loss per share would have been $31,236,000 and $1.05 per share, respectively.

(3)

Includes restricted cash of $4 million at June 30, 2001.

15

COMPARATIVE PER SHARE INFORMATION (UNAUDITED)

    The following table summarizes per share information for Applera and Axys on a historical and unaudited pro forma basis for Applera and a historical and equivalent pro forma basis for Axys. The following information should be read in conjunction with the audited consolidated financial statements of Applera, which are incorporated herein by reference, the audited financial statements of Axys, the unaudited interim financial statements of Axys, the selected historical consolidated and consolidating financial information of Applera and Axys, the selected unaudited pro forma consolidated and consolidating financial information and the unaudited pro forma condensed consolidated and consolidating financial statements included elsewhere in this proxy statement/prospectus. The pro forma information is presented for illustrative purposes only and is not necessarily indicative of the operating results or financial position that would have occurred if the merger had been consummated as of the beginning of the periods presented, nor is it necessarily indicative of the future operating results or financial position of the combined companies.

16

(1)

The Axys per share equivalent pro forma information is calculated by multiplying the per share amounts for the Celera Genomics group by 0.1355, which is the exchange ratio that would have been applied to the Axys common stock under the merger agreement had the merger occurred on October 1, 2001. If the merger had occurred on October 1, 2001, the average closing price of
Applera—Celera stock during the calculation period that would have been used in the determination of the exchange ratio was $21.38. The pro forma per share information may differ if the ten-day average closing price of Applera—Celera stock exceeds $34.32 per share prior to the closing of the merger.

17

COMPARATIVE PER SHARE MARKET PRICE AND DIVIDEND INFORMATION

    Applera—Celera stock is listed on the New York Stock Exchange under the symbol: "CRA."

    The following table sets forth the range of high and low sale prices of Applera—Celera stock as reported by the New York Stock Exchange Composite Tape since May 6, 1999. On May 6, 1999, Applera recapitalized and issued two new classes of stock, the Applera—Celera stock and the Applera—Applied Biosystems stock, to the stockholders of Applera's predecessor. Effective November 30, 2000, Applera, which was named "PE Corporation" at the time of the recapitalization, was renamed "Applera Corporation," and the Applied Biosystems group, which was named the "PE Biosystems" group at the time of the recapitalization, was renamed the "Applied Biosystems" group. Therefore, neither the Applera—Celera stock nor the Applera—Applied Biosystems stock was issued or outstanding at any time prior to May 6, 1999. The table gives effect to the two-for-one stock split of Applera—Celera stock effected in the form of a 100% stock dividend distributed on February 18, 2000. Applera has not paid any cash dividends with respect to Applera—Celera stock and does not anticipate paying any cash dividends on Applera—Celera stock in the foreseeable future.

18

    Axys common stock is traded on the Nasdaq National Market under the symbol "AXPH."

    The following table sets forth the range of high and low sale prices of Axys common stock as reported on the Nasdaq National Market since January 7, 1998, the date when Arris Pharmaceuticals Corporation and Sequana Therapeutics merged to form Axys. Axys has not paid any cash dividends since its inception and does not anticipate paying any cash dividends in the foreseeable future.