Ann-Charlotte Berglund Sonnhammer

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Gene tree and species tree reconstruction, orthology analysis and reconciliation, are problems important in multigenome-based comparative genomics and biology in general. In the present paper, we advance the frontier of these areas in several respects and provide important computational tools. First, exact algorithms are given for several probabilistic(More)
The InParanoid eukaryotic ortholog database ( has been updated to version 6 and is now based on 35 species. We collected all available 'complete' eukaryotic proteomes and Escherichia coli, and calculated ortholog groups for all 595 species pairs using the InParanoid program. This resulted in 2 642 187 pairwise ortholog groups in(More)
MOTIVATION Comparative genomics in general and orthology analysis in particular are becoming increasingly important parts of gene function prediction. Previously, orthology analysis and reconciliation has been performed only with respect to the parsimony model. This discards many plausible solutions and sometimes precludes finding the correct one. In many(More)
BACKGROUND Evolutionary processes, such as gene family evolution or parasite-host co-speciation, can often be viewed as a tree evolving inside another tree. Relating two given trees under such a constraint is known as reconciling them. Adequate software tools for generating illustrations of tree reconciliations are instrumental for presenting and(More)
The fast development of new experimental biotechnologies has resulted in an avalanche of genomic data. As a consequence, the life sciences are becoming more quantitative, and information technology, mathematics and statistics are being incorporated in a natural way. New fields such as bioinformatics and computational biology have emerged and are now key(More)
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