PrIME: Probabilistic Integrated Models of Evolution

Products

PrIMETV: A Tree reconciliation Viewer.: This software was for a time known as "Dart", but a naming conflict has made us change the name.
primeGEM: Probabilistic orthology analysis.
map_dp: Factorizing branchlengths into time and rates.
PrIME-GSR: Gene tree analysis using a Bayesian integrated model for genes, sequences, and rates

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BibTeX for these publications is available.

Åkerborg Ö, Sennblad B, Arvestad L, Lagergren J (2009) Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci U S A 106(14), 5714—5719
Lars Arvestad, Jens Lagergren, and Bengt Sennblad, The gene evolution model and computing its associated probabilities , J ACM, 2009, 56(2):1-44.
Åkerborg Ö, Sennblad B, Lagergren J (2008) Birth-death prior on phylogeny and speed dating. BMC Evol Biol 8, 77
Sennblad B, Schreil E, Berglund Sonnhammer AC, Lagergren J, Arvestad L (2007) primetv: a viewer for reconciled trees. BMC Bioinformatics 8, 148
Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, and Bengt Sennblad, Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution, RECOMB04. (PDF)
Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, and Bengt Sennblad, Bayesian Gene/Species Tree Reconciliation and Orthology Analysis Using MCMC. Bioinformatics 2003, 19 Suppl 1:I7-I15. Presented at ISMB2003. (PDF)