A feud over Emily Dickinson's literary legacy, which has been simmering for generations, came to a boil this week after thousands of the poet's manuscripts were published online.

On one side sits Harvard's Houghton Library with its collection of manuscripts once owned by Susan Dickinson, Emily's confidante and the wife of her brother, Austin. On the other is the library at Amherst College with the papers which Austin's mistress, Mabel Loomis Todd, used to make the first published collection of Dickinson's poems after her death in 1886.

Harvard is accused of shaping the initiative, which it has part-financed, to reinforce the status of Ralph Franklin's 1998 edition of Dickinson's poems – published by Harvard University Press – as the definitive collection of her work.

"This whole project is a gigantic missed opportunity. Instead of revealing the true complexity of Dickinson's manuscript practice and her poetry, the Emily Dickinson Archive re-affirms that Franklin is the single authoritative source when it comes to defining the parameters of Dickinson's poetry," Mike Kelly, head of archives and special collections at Amherst College said. "I understand that the plan is to proceed to another phase of the project that focuses on the letters, but there are dozens of manuscripts that defy any sort of classification and problematise the current scheme. Here was an opportunity to peel back the layers of interpretation and classification that have built up over the years and get back to the original documents."

The Emily Dickinson Archive includes only 539 of the 850 manuscripts held by Amherst, which are freely available for readers through its digital collections archive.

"Several members of the board, myself included, argued that the site should either include all of the manuscripts or it should be more honest in describing its actual parameters," Kelly said.

The Emily Dickinson Archive allows readers to find manuscript versions of her poems from collections held at Harvard, Amherst, Boston Public Library and five other institutions. According to the site's description, it aspires to "make available in one virtual place those resources that seem central to the study of Dickinson's work: images of her manuscripts; a selection of editions of those manuscripts; and selected print and electronic resources that serve as a starting point for the study of Dickinson's manuscripts".

"We felt it best to start with a subset of Emily Dickinson's work," said Leslie Morris, Harvard curator of modern books and manuscripts. "The poems; defined by the edition that included the most poems; and to see how the site worked for a variety of people."

Harvard has positioned the archive as open to changes and revisions at a later date. "The advantage of electronic archives is that they are fluid, and expandable. We also plan to make the application programming interface (API) open, which will enable others to use the EDA in other ways. So what you see right now isn't the archive in its entirety, just the first step." An API is a kind of library which explains how components of computer software interact together, which can be publicly shared to enable anyone to develop new ways of working with the archive's materials or its technology infrastructure.

For the Dickinson biographer Lyndall Gordon, a senior research fellow at St Hilda's college, Oxford, the situation reveals "a war between the two houses which is extraordinarily, pulsatingly alive in the present, and has been handed down from generation to generation".

"It all goes back to the adultery and the two homes," she said. "Austin had an explosive affair with Mabel Loomis Todd, an incredibly accomplished young woman who arrived in Amherst beautifully dressed and was taken in by Susan Dickinson. It's a classic story. Todd had a trained voice, was a terrific reader and published short stories. But she was malicious, and she maligned Susan, and so it became embittered very quickly."