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Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
Huerta-Cepas, J. and Forslund, K. and Coelho, L.P. and Szklarczyk, D. and Jensen, L.J. and von Mering, C. and Bork, P.
Molecular Biology and Evolution 34 (8): 2115-2122. 1 August 2017

ETE 3: reconstruction, analysis and visualization of phylogenomic data.
Huerta-Cepas, J. and Serra, F. and Bork, P.
Molecular Biology and Evolution 33 (6): 1635-1638. June 2016

Bio++: efficient extensible libraries and tools for computational molecular evolution.
Gueguen, L. and Gaillard, S. and Boussau, B. and Gouy, M. and Groussin, M. and Rochette, N.C. and Bigot, T. and Fournier, D. and Pouyet, F. and Cahais, V. and Bernard, A. and Scornavacca, C. and Nabholz, B. and Haudry, A. and Dachary, L. and Galtier, N. and Belkhir, K. and Dutheil, J.Y.
Molecular Biology and Evolution 30 (8): 1745-1750. August 2013

Differential evolution of the 13 Atlantic salmon Hox clusters.
Mungpakdee, S. and Seo, H.C. and Angotzi, A.R. and Dong, X. and Akalin, A. and Chourrout, D.
Molecular Biology and Evolution 25 (7): 1333-1343. July 2008

Domain tree-based analysis of protein architecture evolution.
Forslund, K. and Henricson, A. and Hollich, V. and Sonnhammer, E.L.L.
Molecular Biology and Evolution 25 (2): 254-264. 1 February 2008

QNet: an agglomerative method for the construction of phylogenetic networks from weighted quartets.
Grünewald, S. and Forslund, K. and Dress, A. and Moulton, V.
Molecular Biology and Evolution 24 (2): 532-538. 1 February 2007

An evolutionary model for protein-coding regions with conserved RNA structure.
Pedersen, J.S. and Forsberg, R. and Meyer, I.M. and Hein, J.
Molecular Biology and Evolution 21 (10): 1913-1922. October 2004

The frequency distribution of gene family sizes in complete genomes.
Huynen, M.A. and van Nimwegen, E.
Molecular Biology and Evolution 15 (5): 583-589. 1 May 1998


Advances and applications in the quest for orthologs.
Glover, N. and Dessimoz, C. and Ebersberger, I. and Forslund, S.K. and Gabaldón, T. and Huerta-Cepas, J. and Martin, M.J. and Muffato, M. and Patricio, M. and Pereira, C. and Sousa da Silva, A. and Wang, Y. and Sonnhammer, E. and Thomas, P.D.
Molecular Biology and Evolution 36 (10): 2157-2164. October 2019


A mitochondrial ancestry of the hydrogenosomes of Nyctotherus ovalis.
van Hoek, A.H.A.M. and Akhmanova, A.S. and Huynen, M.A. and Hackstein, J.H.P.
Molecular Biology and Evolution 17 (1): 202-206. 1 January 2000

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