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UFBoot2: Improving the Ultrafast Bootstrap Approximation.
Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. Hoang DT, et al. Among authors: von haeseler a. Mol Biol Evol. 2018 Feb 1;35(2):518-522. doi: 10.1093/molbev/msx281. Mol Biol Evol. 2018. PMID: 29077904 Free PMC article.
Sample size for a phylogenetic inference.
Churchill GA, von Haeseler A, Navidi WC. Churchill GA, et al. Among authors: von haeseler a. Mol Biol Evol. 1992 Jul;9(4):753-69. doi: 10.1093/oxfordjournals.molbev.a040757. Mol Biol Evol. 1992. PMID: 1630311
A statistical test based on a multinomial model for character-state configurations is described. The importance of including invariable sites in models for sequence change is demonstrated, and their effect on sample size is quantified. The methods are applied to
A statistical test based on a multinomial model for character-state configurations is described. The importance of including i
Methods for inferring phylogenies from nucleic acid sequence data by using maximum likelihood and linear invariants.
Navidi WC, Churchill GA, von Haeseler A. Navidi WC, et al. Among authors: von haeseler a. Mol Biol Evol. 1991 Jan;8(1):128-43. doi: 10.1093/oxfordjournals.molbev.a040633. Mol Biol Evol. 1991. PMID: 2002762
The method of linear invariants described by Cavender, which includes Lake's method of evolutionary parsimony as a special case, is essentially a form of the likelihood-ratio method. In the case of a small number of species (four or five), these methods may b …
The method of linear invariants described by Cavender, which includes Lake's method of evolutionary parsimony as a special case, is e …
Quartet-mapping, a generalization of the likelihood-mapping procedure.
Nieselt-Struwe K, von Haeseler A. Nieselt-Struwe K, et al. Among authors: von haeseler a. Mol Biol Evol. 2001 Jul;18(7):1204-19. doi: 10.1093/oxfordjournals.molbev.a003907. Mol Biol Evol. 2001. PMID: 11420361
Here we analyze the special case of a four-species tree generated under a range of evolution models and compare the results with those of a natural extension of the likelihood-mapping approach, geometry-mapping (GM), which is based on the method of statistica …
Here we analyze the special case of a four-species tree generated under a range of evolution models and compare the results wi …
Assessing variability by joint sampling of alignments and mutation rates.
Metzler D, Fleissner R, Wakolbinger A, von Haeseler A. Metzler D, et al. Among authors: von haeseler a. J Mol Evol. 2001 Dec;53(6):660-9. doi: 10.1007/s002390010253. J Mol Evol. 2001. PMID: 11677626
When two sequences are aligned with a single set of alignment parameters, or when mutation parameters are estimated on the basis of a single "optimal" sequence alignment, the variability of both the alignment and the estimated parameters can be seriously underestima …
When two sequences are aligned with a single set of alignment parameters, or when mutation parameters are estimated on the basis of …
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.
Schmidt HA, Strimmer K, Vingron M, von Haeseler A. Schmidt HA, et al. Among authors: von haeseler a. Bioinformatics. 2002 Mar;18(3):502-4. doi: 10.1093/bioinformatics/18.3.502. Bioinformatics. 2002. PMID: 11934758
SUMMARY: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. ...To run the parallel version of PUZZLE, a Message Passing Interface (MPI) library has to be install …
SUMMARY: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and …
Identifying site-specific substitution rates.
Meyer S, von Haeseler A. Meyer S, et al. Among authors: von haeseler a. Mol Biol Evol. 2003 Feb;20(2):182-9. doi: 10.1093/molbev/msg019. Mol Biol Evol. 2003. PMID: 12598684
A maximum likelihood framework for estimating site-specific substitution rates is presented that does not require any prior assumptions about the rate distribution. ...The method is applied to the complete mitochondrial DNA sequence of 53 humans, providing a complet
A maximum likelihood framework for estimating site-specific substitution rates is presented that does not require any prior assumptio
Testing substitution models within a phylogenetic tree.
Weiss G, von Haeseler A. Weiss G, et al. Among authors: von haeseler a. Mol Biol Evol. 2003 Apr;20(4):572-8. doi: 10.1093/molbev/msg073. Epub 2003 Apr 2. Mol Biol Evol. 2003. PMID: 12679552 Review.
To test this assumption statistically, we propose a test based on the sample covariance matrix of the set of substitution rate matrices estimated from pairwise sequence comparison. The sample covariance matrix is condensed into a one-dimensional test statistic Delta …
To test this assumption statistically, we propose a test based on the sample covariance matrix of the set of substitution rate matric …
IQPNNI: moving fast through tree space and stopping in time.
Vinh le S, Von Haeseler A. Vinh le S, et al. Among authors: von haeseler a. Mol Biol Evol. 2004 Aug;21(8):1565-71. doi: 10.1093/molbev/msh176. Epub 2004 May 26. Mol Biol Evol. 2004. PMID: 15163768
An efficient tree reconstruction method (IQPNNI) is introduced to reconstruct a phylogenetic tree based on DNA or amino acid sequence data. ...Moreover, we suggest a rule which indicates when to stop the search. Simulations show that IQPNNI gives a slightly b …
An efficient tree reconstruction method (IQPNNI) is introduced to reconstruct a phylogenetic tree based on DNA or amino acid sequence …
Simultaneous statistical multiple alignment and phylogeny reconstruction.
Fleissner R, Metzler D, von Haeseler A. Fleissner R, et al. Among authors: von haeseler a. Syst Biol. 2005 Aug;54(4):548-61. doi: 10.1080/10635150590950371. Syst Biol. 2005. PMID: 16085574
In this paper we present and discuss a strategy based on simulated annealing, which makes use of these models to infer a phylogenetic tree for a set of DNA or protein sequences together with the sequences'indel history, i.e., their multiple alignment augmente …
In this paper we present and discuss a strategy based on simulated annealing, which makes use of these models to infer a phylo …
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