| 1.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 | I have reviewed this    quarterly report on Form 10-Q of Applera Corporation; |
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|   2.Based on my knowledge, this    report does not contain any untrue statement of a material fact or omit to    state a material fact necessary to make the statements made, in light of the    circumstances under which such statements were made, not misleading with    respect to the period covered by this report;   3.Based on my knowledge, the    financial statements, and other financial information included in this    report, fairly present in all material respects the financial condition,    results of operations and cash flows of the registrant as of, and for, the    periods presented in this report;  4.The registrant’s other    certifying officer(s) and I are responsible for establishing and maintaining    disclosure controls and procedures (as defined in Exchange Act Rules    13a-15(e) and 15d-15(e)) and internal control over financial reporting (as    defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and    have:   (a)Designed such disclosure    controls and procedures, or caused such disclosure controls and procedures to    be designed under our supervision, to ensure that material information    relating to the registrant, including its consolidated subsidiaries, is made    known to us by others within those entities, particularly during the period    in which this report is being prepared;    (b)Designed such internal    control over financial reporting, or caused such internal control over    financial reporting to be designed under our supervision, to provide    reasonable assurance regarding the reliability of financial reporting and the    preparation of financial statements for external purposes in accordance with    generally accepted accounting principles;    (c)Evaluated the effectiveness    of the registrant’s disclosure controls and procedures and presented in this    report our conclusions about the effectiveness of the disclosure controls and    procedures, as of the end of the period covered by this report based on such    evaluation; and    (d)Disclosed in this report    any change in the registrant’s internal control over financial reporting that    occurred during the registrant’s most recent fiscal quarter (the registrant’s    fourth fiscal quarter in the case of an annual report) that has materially    affected, or is reasonably likely to materially affect, the registrant’s    internal control over financial reporting; and   5.The registrant’s other    certifying officer(s) and I have disclosed, based on our most recent    evaluation of internal control over financial reporting, to the registrant’s    auditors and the audit committee of the registrant’s board of directors (or    persons performing the equivalent functions):   (a)All significant    deficiencies and material weaknesses in the design or operation of internal    control over financial reporting which are reasonably likely to adversely    affect the registrant’s ability to record, process, summarize and report    financial information; and    (b)Any fraud, whether or not    material, that involves management or other employees who have a significant    role in the registrant’s internal control over financial reporting. Date:   November 9, 2005  /s/ Dennis L. Winger  Chief Financial Officer  |