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Welcome to project loft

René TJM van der Heijden, Berend Snel, Vera van Noort and Martijn A Huynen
Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands

Abstract Background: Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature of phylogenetic relations results in inparalogs and outparalogs. For situations with more than two species we lack semantics to specifically describe the phylogenetic relations, let alone to exploit them. Published procedures to extract orthologous groups from phylogenetic trees do not allow identification of orthology at various levels of resolution, nor do they document the relations between the orthologous groups.

Results: We introduce "levels of orthology" to describe the multi-level nature of gene relations. This is implemented in a program LOFT (Levels of Orthology From Trees) that assigns hierarchical orthology numbers to genes based on a phylogenetic tree. To decide upon speciation and gene duplication events in a tree LOFT can be instructed either to perform classical species-tree reconciliation or to use the species overlap between partitions in the tree. The hierarchical orthology numbers assigned by LOFT effectively summarize the phylogenetic relations between genes. The resulting high-resolution orthologous groups are depicted in colour, facilitating visual inspection of (large) trees. A benchmark for orthology prediction, that takes into account the varying levels of orthology between genes, shows that the phylogeny-based high-resolution orthology assignments made by LOFT are reliable.

Conclusion: The "levels of orthology" concept offers high resolution, reliable orthology, while preserving the relations between orthologous groups. A Windows as well as a preliminary Java version of LOFT is available from svn co https://trac.nbic.nl/svn/loft loft or http://www.cmbi.ru.nl/LOFT

The original publication is available

Mailing lists

This project provides the following mailing lists.

  • loft-users: a list intended for general discussion on the project.
  • loft-commits: a list that receives source code commit messages.
  • loft-devel: a list intended for discussion among developers (subscription is restricted to registered developers).

Source access

If available, anonymous readonly subversion access works as follows:

  svn co https://trac.nbic.nl/svn/loft loft

Write access is only available to registered developers.

You can become a developer by registering yourself if you haven't already done so, and requesting write access on the loft-users mailing list.

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Last modified 7 years ago Last modified on Mar 14, 2011, 2:32:19 PM