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IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. Nguyen LT, et al. Among authors: schmidt ha. Mol Biol Evol. 2015 Jan;32(1):268-74. doi: 10.1093/molbev/msu300. Epub 2014 Nov 3. Mol Biol Evol. 2015. PMID: 25371430 Free PMC article.
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.
Schmidt HA, Strimmer K, Vingron M, von Haeseler A. Schmidt HA, et al. Bioinformatics. 2002 Mar;18(3):502-4. doi: 10.1093/bioinformatics/18.3.502. Bioinformatics. 2002. PMID: 11934758
pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies.
Minh BQ, Vinh le S, von Haeseler A, Schmidt HA. Minh BQ, et al. Among authors: schmidt ha. Bioinformatics. 2005 Oct 1;21(19):3794-6. doi: 10.1093/bioinformatics/bti594. Epub 2005 Jul 26. Bioinformatics. 2005. PMID: 16046495
pIPHULA--parallel inference of population parameters using a likelihood approach.
Schmidt HA, von Haeseler A, Buschbom J. Schmidt HA, et al. Bioinformatics. 2007 Oct 1;23(19):2636-7. doi: 10.1093/bioinformatics/btm391. Epub 2007 Aug 12. Bioinformatics. 2007. PMID: 17698495
Maximum-likelihood analysis using TREE-PUZZLE.
Schmidt HA, von Haeseler A. Schmidt HA, et al. Curr Protoc Bioinformatics. 2007 Mar;Chapter 6:Unit 6.6. doi: 10.1002/0471250953.bi0606s17. Curr Protoc Bioinformatics. 2007. PMID: 18428792
Rooted triple consensus and anomalous gene trees.
Ewing GB, Ebersberger I, Schmidt HA, von Haeseler A. Ewing GB, et al. Among authors: schmidt ha. BMC Evol Biol. 2008 Apr 25;8:118. doi: 10.1186/1471-2148-8-118. BMC Evol Biol. 2008. PMID: 18439266 Free PMC article.
Accuracy of phylogeny reconstruction methods combining overlapping gene data sets.
Kupczok A, Schmidt HA, von Haeseler A. Kupczok A, et al. Among authors: schmidt ha. Algorithms Mol Biol. 2010 Dec 6;5:37. doi: 10.1186/1748-7188-5-37. Algorithms Mol Biol. 2010. PMID: 21134245 Free PMC article.
Comparative Genomics Identifies Epidermal Proteins Associated with the Evolution of the Turtle Shell.
Holthaus KB, Strasser B, Sipos W, Schmidt HA, Mlitz V, Sukseree S, Weissenbacher A, Tschachler E, Alibardi L, Eckhart L. Holthaus KB, et al. Among authors: schmidt ha. Mol Biol Evol. 2016 Mar;33(3):726-37. doi: 10.1093/molbev/msv265. Epub 2015 Nov 24. Mol Biol Evol. 2016. PMID: 26601937 Free PMC article.
Corrigendum to: IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. Minh BQ, et al. Among authors: schmidt ha. Mol Biol Evol. 2020 Aug 1;37(8):2461. doi: 10.1093/molbev/msaa131. Mol Biol Evol. 2020. PMID: 32556291 Free PMC article. No abstract available.
Distinguishing Felsenstein zone from Farris zone using neural networks.
Leuchtenberger AF, Crotty SM, Drucks T, Schmidt HA, Burgstaller-Muehlbacher S, von Haeseler A. Leuchtenberger AF, et al. Among authors: schmidt ha. Mol Biol Evol. 2020 Jul 8:msaa164. doi: 10.1093/molbev/msaa164. Online ahead of print. Mol Biol Evol. 2020. PMID: 32637998
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