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Jeremy Allison, a high-profile open-source programmer, has resigned from Novell because of objections over its patent deal with Microsoft and is moving to Google.

In his resignation letter, Allison said Novell’s patent pact with Microsoft has crippled the Linux seller’s relations with the open-source community. At Google, he’ll continue his work on Samba, the open-source project he helped launch. Samba is software that lets Linux servers share files on Windows networks.

“Whilst the Microsoft patent agreement is in place there is nothing we can do to fix community relations…Until the patent provision is revoked, we are pariahs,” Allison said in the letter, quoting from an earlier message he sent to Novell management. Allison joined Novell in 2005 after working at Hewlett-Packard.

Groklaw, a site that monitors open-source legal affairs, published Allison’s resignation letter on Thursday. On the same day Allison confirmed the letter’s authenticity, saying he had sent it to internal Novell mailing list, but declined to comment further on his departure from Novell.

Google is a major open-source software user and participates in several open-source programming projects. Andrew Morton, a key lieutenant to Linux leader Linus Torvalds, works there, though his salary is paid by the Open Source Development Labs.

Novell spokesman Bruce Lowry declined to comment on Allison’s views, but said the company still employs two Samba programmers. “We wish him the best,” Lowry said.

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Novell said Monday it is participating in an open-source project designed to bridge rival document formats and thus enable its OpenOffice.org customers to work with Microsoft Office documents.

Novell, a business software maker, distributes its own edition of the open-source desktop productivity suite OpenOffice. The programs in it save documents in the OpenDocument format, or ODF, which is a standard created by several companies.

By January, Novell said, users of the OpenOffice word processor will be able to read documents saved in the Office Open XML format, the default setting for Microsoft’s recently released Office 2007 suite.

“OpenOffice.org is very important to Novell. And as our customers deploy Linux desktops across their organizations, they’re telling us that sharing documents between OpenOffice.org and Microsoft Office is a must-have,” Nat Friedman, Novell’s chief technology and strategy officer for open source, said in a statement.

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Just weeks after its controversial patent cooperation agreement with Microsoft, Novell is hitting out at statements made by Microsoft executives that the deal acknowledges that Linux infringes on its intellectual property.

Novell has been under fire from many members of the Linux and open-source community since entering into a set of broad collaboration agreements with Microsoft to build, market and support a series of new solutions that will make Novell and Microsoft products work better together, including providing each other’s customers with patent coverage for their respective products.

Recent statements from Microsoft officials such as CEO Steve Ballmer that the deal effectively acknowledges that Linux infringes on his company’s intellectual property have exacerbated these criticisms from the open-source community.

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