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ALF--a simulation framework for genome evolution.
Mol Biol Evol. 2012 Apr;29(4):1115-23. doi: 10.1093/molbev/msr268. Epub 2011 Dec 8.
Mol Biol Evol. 2012.
PMID: 22160766
Free PMC article.
The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study.
Dalquen DA, Altenhoff AM, Gonnet GH, Dessimoz C.
Dalquen DA, et al.
PLoS One. 2013;8(2):e56925. doi: 10.1371/journal.pone.0056925. Epub 2013 Feb 25.
PLoS One. 2013.
PMID: 23451112
Free PMC article.
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Bidirectional best hits miss many orthologs in duplication-rich clades such as plants and animals.
Dalquen DA, Dessimoz C.
Dalquen DA, et al.
Genome Biol Evol. 2013;5(10):1800-6. doi: 10.1093/gbe/evt132.
Genome Biol Evol. 2013.
PMID: 24013106
Free PMC article.
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Standardized benchmarking in the quest for orthologs.
Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M; Quest for Orthologs consortium; Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C.
Altenhoff AM, et al. Among authors: dalquen da.
Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830. Epub 2016 Apr 4.
Nat Methods. 2016.
PMID: 27043882
Free PMC article.
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OMA standalone: orthology inference among public and custom genomes and transcriptomes.
Altenhoff AM, Levy J, Zarowiecki M, Tomiczek B, Warwick Vesztrocy A, Dalquen DA, Müller S, Telford MJ, Glover NM, Dylus D, Dessimoz C.
Altenhoff AM, et al. Among authors: dalquen da.
Genome Res. 2019 Jul;29(7):1152-1163. doi: 10.1101/gr.243212.118. Epub 2019 Jun 24.
Genome Res. 2019.
PMID: 31235654
Free PMC article.
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Gene copy number variation and its significance in cyanobacterial phylogeny.
Schirrmeister BE, Dalquen DA, Anisimova M, Bagheri HC.
Schirrmeister BE, et al. Among authors: dalquen da.
BMC Microbiol. 2012 Aug 15;12:177. doi: 10.1186/1471-2180-12-177.
BMC Microbiol. 2012.
PMID: 22894826
Free PMC article.
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Coalescent Analysis of Phylogenomic Data Confidently Resolves the Species Relationships in the Anopheles gambiae Species Complex.
Thawornwattana Y, Dalquen D, Yang Z.
Thawornwattana Y, et al.
Mol Biol Evol. 2018 Oct 1;35(10):2512-2527. doi: 10.1093/molbev/msy158.
Mol Biol Evol. 2018.
PMID: 30102363
Free PMC article.
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Maximum Likelihood Implementation of an Isolation-with-Migration Model for Three Species.
Dalquen DA, Zhu T, Yang Z.
Dalquen DA, et al.
Syst Biol. 2017 May 1;66(3):379-398. doi: 10.1093/sysbio/syw063.
Syst Biol. 2017.
PMID: 27486180
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