Publications by Dirk Metzler
- R. Roussou, D. Metzler, F. Padovani, F. Thoma, R. Schwarz, B. Shraiman, K.M. Schmoller, C. Osman (2024) Real-time assessment of mitochondrial DNA heteroplasmy dynamics at the single-cell level. EMBO J
- U. Knief, I.A. Müller, K.F. Stryjewski, D. Metzler, M.D. Sorenson, J.B.W. Wolf (2024) Evolution of chromosomal inversions across an avian radiation Molecular Biology and Evolution 41(6): msae092
- R.E. Rollins, G. Margos, A. Brachmann, S. Krebs, A. Mouchet, N.J. Dingemanse, A. Laatamna, N. Reghaissia, V. Fingerle, D. Metzler, N.S. Becker, and L. Chitimia-Dobler (2023) German Ixodes inopinatus samples may not actually represent this tick species International Journal for Parasitology 53(13): 751-761
- V.M. Warmuth, D. Metzler and V. Zamora-Gutierrez (2023) Human disturbance increases coronavirus prevalence in bats Science Advances 9(13): eadd0688
- J. Marquardt, A. Blanckaert, R. Nichols, S.W. Ansell, M. Ruhsam, P.M. Hollingsworth, D. Metzler, H. Schneider, A.R. Leitch (2022) Cyto-nuclear incompatibilities across a bluebell hybrid zone in northern Spain do not prevent genome-wide introgression of neutral markers Evolutionary Journal of the Linnean Society 1: 1-18
- M. Hutzenthaler, F. Jordan and D. Metzler (2022) Costly defense traits in structured populations ALEA, Lat. Am. J. Probab. Math. Stat. 19: 1697–1752
- P. Kerbs, S. Vosberg, S. Krebs, A. Graf, H. Blum, A. Swobodak, A.M.N. Batcha, U. Mansmann, D. Metzler, C.A. Heckman, T. Herold, P.A. Greif (2022) Fusion gene detection by RNA-sequencing complements diagnostics of acute myeloid leukemia and identifies recurring NRIP1-MIR99AHG rearrangements Haematologica 107
- D. Metzler, U. Knief, J. Penalba, J.B.W. Wolf (2021) Assortative mating and epistatic mating-trait architecture induce complex movement of the crow hybrid zone Evolution 75: 3154-3174
- M. Hutzenthaler and D. Metzler (2021) Evolution of altruistic defence traits in structured populations In: Probabilistic Structures in Evolution (Eds.: E. Baake, A. Wakolbinger) European Mathematical Society Publishing House
- V.A. Rohr, T. Volkmer, D. Metzler, C. Kuepper (2021) Neoptile feathers contribute to outline concealment of precocial chicks Scientific Reports 11: 5483
- K. Grosser, D. Metzler (2020) Modeling methylation dynamics with simultaneous changes in CpG islands BMC Bioinformatics 21: 115
- P. Kerbs, A.M. Batcha, A. M. Nazeer and Vosberg, S. and Metzler, D. and Herold, Tobias and Greif, P. A. (2019) Gene Fusion Detection by RNA-SEQ In Acute Myeloid Leukemia (AML) Blood 134 (Suppl. 1): 4655
- V.M. Link, C.E. Romanoski, D. Metzler, C.K. Glass (2018) MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements Nucleic Acids Research gky491
- V.M. Link, S. Duttke, H. Chun, I. Holtman, E. Westin, M. Hoeksema, Y. Abe,D. Skola, C. Romanoski, J. Tao, G. Fonseca, T. Troutman, N. Spann, T. Strid, M. Sakai, M. Yu, R. Hu, F. Fang, D. Metzler, B. Ren, C.K. Glass (2018) Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Cell 173:1796-1809
- M.J. Wittmann, H. Stuis, D. Metzler (2018) Genetic Allee effects and
their interaction with ecological Allee effects
Journal of Animal Ecology 87:11--23 - K.C. Wollenberg Valero, J. Garcia-Porta, A. Rodriguez, M. Arias, A. Shah, R.D. Randrianiaina, J.L. Brown, F. Glaw, F. Amat, S. Künzel, D. Metzler, R.D. Isokpehi, M. Vences (2017) Transcriptomic and macroevolutionary evidence
for phenotypic uncoupling between frog life history phases.
Nature Communications 8:15213 - F. Grandke, S. Ranganathan, N. van Bers, J.R. de Haan, D. Metzler (2017) PERGOLA: Fast and deterministic linkage mapping of polyploids
BMC Bioinformatics 18:12 - X. Gong, L. Bräcker, N. Bölke, C. Plata, S. Zeitlmayr, D. Metzler, K. Olbricht, N. Gompel, M. Parniske (2016) Identification of strawberry accessions with reduced emergence rates of the pest Drosophila suzukii
Front. Plant Sci. 7:1880. doi: 10.3389/fpls.2016.01880 -
D. Metzler, F. Jordan, T. Pamminger, S. Foitzik (2016) The influence of space and time on the evolution of altruistic defense: the case of ant slave rebellion
Journal of Evolutionary Biology 29: 874–886 -
P. Staab, D. Metzler (2016) coala: An R framework for coalescent simulation
Bioinformatics 32(12): 1903-1904 -
F. Grandke, P. Singh, H.C.M. Heuven, J.R. de Haan, D. Metzler (2016)
Advantages of continuous genotype values over genotype classes for GWAS in
higher polyploids: a comparative study in hexaploid chrysanthemum
BMC Genomics 17:672 -
W. von Thienen, D. Metzler, V. Witte (2016)
How memory and motivation modulate the responses to trail pheromones in three ant species
Behavioral Ecology and Sociobiology 70(3): 393-407 -
P. Staab, S. Zhu, D. Metzler, and G. Lunter (2015) scrm: efficiently
simulating long sequences using the approximated coalescent with
recombination
Bioinformatics 31(10): 1680-1682 -
W. von Thienen, D. Metzler, V. Witte (2015)
Modeling shortest path selection of the ant Linepithema humile using
psychophysical theory and realistic parameter values
Journal of Theoretical Biology 372: 168-178 - F. Gatzmann, D. Metzler, S. Krebs, H. Blum, A. Sing, A. Takano,
H. Kawabata, V. Fingerle, G. Margos, N.S. Becker (2015) NGS population
genetics analyses reveal divergent evolution of a Lyme Borreliosis agent in
Europe and Asia
Ticks and Tick-Borne Diseases 6(3): 344-351 - M.J. Wittmann, W. Gabriel, D. Metzler (2014)
Genetic diversity in introduced populations with Allee effect
Genetics 198: 299-310 - M.J. Wittmann, W. Gabriel, D. Metzler (2014)
Population genetic consequences of the Allee effect and the role of
offspring-number variation
Genetics 198: 311-320 -
T. Pamminger, S. Foitzik, D. Metzler, P.S. Pennings (2014) Oh sister, where
art thou? Spatial population structure and the
evolution of an altruistic defence trait
Journal of Evolutionary Biology 27: 2443-56 -
W. von Thienen, D. Metzler, D.-H. Choe, V. Witte (2014) Pheromone
Communication in ants: A Detailed Analysis of Concentration Dependent
Decisions in Three Species
Behavioral Ecology and Sociobiology 68: 1611-1627 -
D.P. Lyras, D. Metzler (2014) ReformAlign: improved multiple sequence
alignments using a profile-based meta-alignment approach
BMC Bioinformatics 15: 265 -
M.J. Wittmann, D. Metzler, W. Gabriel, J.M. Jeschke (2014)
Decomposing propagule pressure: the effects of propagule size and propagule
frequency on invasion success
Oikos 123: 441-450. -
F. Grandke , S. Ranganathan, A. Czech, J.R. de Haan, D. Metzler (2014) Bioinformatic Tools for Polyploid Crops
Journal of Agricultural Science and Technology B 4: 593-601 -
L. Mathew, L. Rose, P. Staab, D. Metzler (2013) Why to account for
finite-sites in population genetic studies and how to do this with Jaatha
2.0.
Ecology and Evolution 3: 3647–3662.
DOI: 10.1002/ece3.722 -
M.J. Wittmann, M. Hutzenthaler, W. Gabriel, D. Metzler (2013) Ecological and
genetic effects of introduced species on their native
competitors.
Theoretical Population Biology 84: 25-35 http://dx.doi.org/10.1016/j.tpb.2012.11.003, preprint version available via arXiv:1208.1294 -
C. Pokalyuk, L. Mathew, D. Metzler, P. Pfaffelhuber (2013) Competing islands limit the rate of adaptation in structured populations
Theoretical Population Biology 90: 1-11. -
M. Linnenbrink, J. Wang, E. Hardouin, S. Künzel, D. Metzler, J. Baines
(2013) The role of biogeography in shaping diversity of the intestinal
microbiota in house mice.
Molecular Ecology 22(7):1904-1916 - G. Doose, D. Metzler (2012) Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots. Bioinformatics 28(17): 2242-2248
-
D. Hoffmann, M. Hutzenthaler, J. Seebach, M. Panning,
A. Umgelter, H. Menzel, U. Protzer, D. Metzler (2012)
Norovirus GII.4 and GII.7 Capsid Sequences Undergo Positive Selection in
Chronically Infected Patients
Infection, Genetics and Evolution. 12: 461-466 - P. Pavlidis, D. Metzler, W. Stephan (2012) Selective Sweeps in Multilocus Models of Quantitative Traits Genetics 192(1) 225-239
- L. Nauheimer, D. Metzler, S.S. Renner (2012) Global history of the ancient monocot family Araceae inferred with models accounting for past continental positions and previous ranges based on fossils. New Phytologist 195(4): 938–950
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T. Karn, L. Pusztai, E. Ruckhäberle, C. Liedtke, V. Müller,
M. Schmidt, D. Metzler, J. Wang, K.R. Coombes, R. Gätje, L. Hanker,
C. Solbach, A. Ahr, U. Holtrich, A. Rody, M. Kaufmann (2012)
Melanoma antigen family A identified by the bimodality index defines a subset
of triple negative breast cancers as candidates for immune response
augmentation
European Journal of Cancer 48(1):12-23 - S. Foitzik, M.H. Rüger, I.M. Kureck, D. Metzler (2011)
Macro- and microgeographic genetic structure in an ant species with
alternative reproductive tactics in sexuals
Journal of Evolutionary Biology 24(12): 2721–30 - L. Naduvilezhath, L.E. Rose, D. Metzler (2011) Jaatha: a fast composite-likelihood approach to estimate demographic parameters
Molecular Ecology 20(13):2709-23 - A. Tellier, P. Pfaffelhuber, B. Haubold, L. Naduvilezhath, L. E. Rose, T. Städler, W. Stephan, and
D. Metzler (2011) Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum
PLoS One 6(5): e18155 - N. Svetec, A. Werzner, R. Wilches, P. Pavlidis,
J.M. Alvarez-Castro, K.W. Broman, D. Metzler, W. Stephan (2011) Identification of X-linked quantitative trait
loci affecting cold tolerance in Drosophila melanogaster and fine
mapping by selective sweep analysis
Molecular Ecology 20(3):530-544 -
A. Rody, T. Karn, C. Liedtke, L. Pusztai, E. Ruckhaeberle, L. Hanker,
R. Gaetje, C. Solbach, A. Ahr, D. Metzler, M. Schmidt, V. Müller,
U. Holtrich, M. Kaufmann (2011)
A clinically relevant gene signature in triple negative and basal-like breast
cancer
Breast Cancer Research 2011 13(5):R97 - S. Foitzik, I. Kureck, M. Rüger, D. Metzler (2010) Alternative
reproductive tactics and the influence of local competition on sex
allocation in the ant Hypoponera opacior.
Behavioral Ecology and Sociobiology 64:1641-1654 -
T. Karn, D. Metzler, E. Ruckhäberle, L. Hanker, R. Gätje,
C. Solbach, A. Ahr, M. Schmidt, U. Holtrich, M. Kaufmann, A. Rody (2010)
Data driven derivation of cutoffs from a pool of 3,030 Affymetrix
arrays to stratify distinct clinical types of breast cancer
Breast Cancer Res Treat 120(3):567-579 - D. Metzler (2010) Book Review: Biostatistics and Microbiology - A Survival Manual. by
D. S. Paulson (Springer, 2008).
Biometrical Journal DOI: 10.1002/bimj.201000033 -
L. Himmelmann, D. Metzler (2009) TreeTime: An extensible C++ software
package for Bayesian phylogeny reconstruction with
time-calibration
Bioinformatics 25(18):2440-2441 doi:10.1093/bioinformatics/btp417, TreeTime homepage - C. A. Hipsley, L. Himmelmann, D. Metzler, J. Mueller (2009)
Integration of Bayesian molecular clock methods and fossil-based soft
bounds reveals early Cenozoic origin of African lacertid lizards
BMC Evolutionary Biology 9:151, doi:10.1186/1471-2148-9-151 -
D. Metzler, R. Fleißner (2009)
Sequence Evolution Models for Simultaneous Alignment and Phylogeny Reconstruction.
In: M.S. Rosenberg (Ed.) Sequence Alignment: Methods, Models, Concepts, and Strategies. University of California Press -
A. Arribas-Gil, D. Metzler, J.-L. Plouhinec (2009) Statistical alignment with a sequence evolution model
allowing rate heterogeneity along the sequence
IEEE/ACM Transactions on Computational Biology and Bioinformatics 6(2): 281-295 -
O. Jurjut, D. Nikolic, G. Pipa, W. Singer, D. Metzler, and
R. Muresan (2009) A color-based visualization technique for
multi-electrode spike trains
Journal of Neurophysiology 102: 3766-3778 - S. Eckerle, V. Brune, C. Döring, E. Tiacci, V. Bohle,
C. Sundström, R. Kodet, M. Paulli, B. Falini, W. Klapper,
A. Baur Chaubert, K. Willenbrock, D. Metzler, Andreas
Bräuninger, R. Küppers, M.-L. Hansmann (2009)
Gene expression profiling of isolated tumor cells from anaplastic
large cell lymphomas:
insights into its cellular origin, pathogenesis and relation to Hodgkin lymphoma
Leukemia 23: 2129-2138 -
E. Ruckhäberle, T. Karn, L. Hanker, R. Gätje, D. Metzler, U. Holtrich, M. Kaufmann, A. Rody (2009)
Prognostic relevance of glucosylceramide synthase (GCS) expression in breast cancer
Journal of Cancer Research and Clinical Oncology 135(1), 81-90 - E. Ruckhäberle, T. Karn, A. Rody, L. Hanker, R. Gätje, D. Metzler, U. Holtrich, M. Kaufmann (2009) Gene expression of ceramide kinase, galactosyl ceramide synthase and ganglioside GD3 synthase is associated with prognosis in breast cancer J. Cancer. Res. Clin. Oncol. 135(8): 1005-1013
- E. Ruckhäberle, U. Holtrich, K. Engels, L. Hanker, R. Gaetje, D. Metzler, T. Karn, A. Rody, M.Kaufmann (2009) Prognostic value of gene expression of ASAH1, LASS4 and LASS6 in breast cancer. Breast 18 Suppl. 1 S29
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A. Rody, T. Karn, E. Ruckhäberle, L. Hanker, D. Metzler,
V. Müller, C. Solbach, A. Ahr, R. Gätje,
U. Holtrich, M. Kaufmann (2009)
Loss of Plexin B1 is highly prognostic in low proliferating ER
positive breast cancers - results of a large
scale microarray analysis
European Journal of Cancer 45 (3), 405-413, http://www.ncbi.nlm.nih.gov/pubmed/19054665 -
A. Rody, U. Holtrich, L. Pusztai, C. Liedtke, R. Gätje, E. Ruckhäberle, C. Solbach, L. Hanker, A. Ahr, D. Metzler, K. Engels, T. Karn, M. Kaufmann (2009)
T-cell metagene predicts a favourable prognosis in estrogen receptor negative and HER2 positive breast cancers
Breast Cancer Research 11:R15 doi:10.1186/bcr2234 -
A. Kovács, B. Turowski, U. Stefenelli, D. Metzler (2009) Primary Tumor Volume as Predicitive Parameter
for Remission after Intraarterial High-dose Cisplatin in Oral and Oropharyngeal Cancer: a Mathematical Model Analysis.
Cranio Maxillofacial Surgery and Orthodontics 3, 174-186 - E. Ruckhäberle, U. Holtrich, K. Engels, L. Hanker, R. Gatje, D. Metzler, T. Karn, M. Kaufmann, A. Rody (2009) Acid ceramidase 1 expression correlates with a better prognosis in ER-positive breast cancer. Climacteric 12(6), 502-513
- M. Löwer, C. Weydig, D. Metzler, A. Reuter, A. Starzinski-Powitz, S. Wessler and G. Schneider (2008)
Prediction of extracellular proteases of the human pathogen Helicobacter pylori reveals proteolytic
activity of the Hp1018/19 protein HtrA
PLoS ONE 3(10): e3510. doi:10.1371/journal.pone.0003510 - V. Brune, E. Tiacci, I. Pfeil, C. Döring, S.
Eckerle, C.J.M. van Noesel, W. Klapper, B. Falini,
A. von Heydebreck, D. Metzler, A. Bräuninger, Martin-Leo
Hansmann, Ralf Küppers (2008) Origin and pathogenesis of nodular
lymphocyte-predominant Hodgkin lymphoma as revealed by global gene
expression analysis
The Journal of Experimental Medicine 205(10), 2251-2268 -
D. Metzler, M. Nebel (2008) Predicting RNA Secondary Structures with Pseudoknots by MCMC Sampling
Journal of Mathematical Biology 56, 161-181
Supplementary Material, see also http://www.informatik.uni-frankfurt.de/~metzler/McQFold - O.F. Jurjut, D. Nikolić, W. Singer, D. Metzler, RC Mureşan (2008) Multidimensional patterns of neuronal activity: how do we see them? BMC Neuroscience 9(1), 1
- A. Rody, U. Holtrich, R. Gatje, V. Müller, M. Gehrmann, K. Engels, S. Loibl, G. von Minckwitz, R. Diallo, D. Metzler, E. Ruckäberle, A. Ahr, C. Solbach, T. Karn, M. Kaufmann (2008) Relevance of stem cell like breast cancers for adjuvant endocrine treatment decision. Onkologie 31 supp. 1, 27
-
L.M. Himmelmann, D. Metzler (2007) A Study on the Empirical Support
for Prior Distributions on Phylogenetic Tree Topologies
in: C. Falter, A. Schliep, J. Selbig, M. Vingron, D. Walther (Eds.) Proceedings of the German Conference on Bioinformatics, September 26-28, 2007, Potsdam, Germany, Lecture Notes in Informatics - Series of the Gesellschaft für Informatik (GI) 115, 101-110 -
M. Frank, C. Döring, D. Metzler, S. Eckerle, M.-L. Hansmann (2007)
Global Gene Expression Profiling of Formalin-Fixed Paraffin-Embedded Tumor Samples:
A Comparison to Snap-Frozen Material Using Oligonucleotide Microarrays
Virchows Archiv 450(6), 699-711 -
K. Engels, S. K. Knauer, D. Metzler, C. Simf, O. Struschka, C. Bier, W. Mann, A. F. Kovacs, R. H.
Stauber (2007) Dynamic intracellular survivin as an early prognostic marker in oral squamous
cell carcinomas: underlying molecular mechanism and potential
Journal of Pathology 211(5), 532-540 -
A. Rody, U. Holtrich, R. Gaetje, M. Gehrmann, K. Engels, G. von Minckwitz, S. Loibl, E. Ruckhäberle,
D. Metzler, A. Ahr, C. Solbach, T. Karn, M. Kaufmann (2007) Poor outcome in estrogen
receptor positive breast cancers predicted by loss of Plexin B1 the receptor for growth repelling
semaphorin 4D
Clinical Cancer Research 13(4), 1115-1122 - K. Engels, S.K. Knauer, D. Metzler, W. Mann, A.F. Kovacs, R.H. Stauber (2007) The distribution of nuclear and cytoplasmic survivin is a predictive marker of survival and sensitivity to chemo- and radiation induced apoptosis in oral squamous cell carcinoma.
Pathology Research and Practice 203(5), 270-271 - V. Brune, I. Pfeil, C. Doering, E. Tiacci, S. Eckerle, C.J.M. Van Noesel, W. Klapper, G. Mechtersheimer, B. Falini, D. Metzler, A. Bräuninger, M.L. Hansmann, R. K¨ppers (2007) Insights into the pathogenesis of primary nodular lymphocyte-predominant Hodgkin lymphoma (NLPH) by global gene expression analysis of isolated L&H cells.
Haematologica – The Haematology Journal 92 Suppl. 5, 40 -
S. Eckerle, V. Brune, C. Doering, E. Tiacci, C. Sundstrom, R. Kodet, M. Paulli, B. Falini, W. Klapper, A.B. Chaubert, D. Metzler, A. Bräuninger, R. Küppers, M.L. Hansmann (2007) Differences and similarities between classical Hodgkin lymphoma and subtypes of anaplastic large cell lymphomas as revealed by global gene expression profiling of microdissected lymphoma cells
Haematologica – The Haematology Journal 92 Suppl. 5, 41 - A.F. Kovacs, B. Turowski, D. Metzler, R. Sader (2007) Tumor volume is a prognostic parameter for remission in oral and oropharyngeal cancer. Oral Oncology 1 Suppl. S, 103
- D. Metzler (2006) Robust E-Values for Gapped Local Alignments
Journal of Computational Biology 13, 882-896 -
D. Metzler, M.E. Nebel (2006) An MCMC-Method for Sampling RNA Secondary Structures with
Pseudoknots.
Proceedings of the IASTED International Conference Computational and Systems Biology, November 13-14, 2006, Dallas, TX, USA. - R. Fleißner, D. Metzler, A. von Haeseler (2005) Simultaneous
Statistical Multiple Alignment and Phylogeny
Reconstruction.
Syst. Biol. 54, 548-561 - D. Metzler (2005) A Poisson Model Heuristic for Judging the Significance of Gapped Local Alignments
Oberwolfach Reports 40 (Proceedings of the Workshop Mathematical Population Genetics, organized by E. Baake, W. Ewens, and A. Wakolbinger), 2277-2279 - D. Metzler, R. Fleißner, A. Wakolinger, A. v. Haeseler (2005)
Stochastic insertion-deletion processes and statistical sequence alignment. MFWvH04.pdf
In: J.D. Deuschel, A. Greven (Eds.) Interacting Stochastic Systems, Springer - D. Metzler
(2003) Statistical Alignment based on fragment insertion and deletion
models.
Bioinformatics19.4 490-499,
see also http://www.math.uni-frankfurt.de/~stoch/software/mcmcsalut/index.html - D. Metzler, S. Grossmann, A. Wakolbinger (2002) A Poisson
model for gapped local alignments.
Stat. Prob. Letters. 60, 91-100
preprint version: localign.pdf (165 kb), localign.ps (230 kb), localign.ps.gz (62 kb) - I. Ebersberger, D. Metzler, C. Schwarz, S. Pääbo (2002)
Genome-wide comparison of DNA sequences between humans and chimpanzees.
Am. J. Hum. Genet. 70 , 1490-1497 - D. Metzler, R. Fleißner, A. Wakolbinger, A. von Haeseler
(2001) Assessing variability by joint sampling of alignments and
mutation rates.
J. Mol. Evol. 53.6 , 660-669; see also http://www.math.uni-frankfurt.de/~stoch/software/mcmcalgn/) - R. Fleißner, D. Metzler, A. von Haeseler (2000)
Can one estimate distances from pairwise sequence alignments?
In: E. Bornberg-Bauer, U. Rost, J. Stoye, M.Vingron (eds.) GCB 2000, Proceedings of the German Conference on Bioinformatics, October 5-7, 2000, Heidelberg, Logos Verlag, Berlin, 89-95 - D. Metzler (1999) Poisson-Approxmationen
für genetische Fingerabdrücke
Dissertation, FB Mathematik der J.W.Goethe-Universität Frankfurt. diss.ps (1529KB), diss.ps.gz (401 KB) - S. Anulova, J. Bennies, J. Lenhard, D. Metzler, Y. Sung, A.
Weber (1999) Six Ways of Looking at Burtins Lemma.
Amer. Math. Monthly, 106.4, 345-351 - B. Schierwater, D. Metzler, K. Krüger, B. Streit (1996)
The Effects of Nested Primer Binding Sites on the Reproducibility
of PCR: Mathematical Modeling and Computer Simulation Studies.
J. Comp. Biol. 3.2, 235-251
Software
for analyzing population genetic data:- Jaatha is an R package for estimating demographic parameters from population genetic data.
- TreeTime is an extensible C++ software package for the Bayesian sampling of phylogenetic trees.
- PhyloQFold is a program for MCMC-sampling conserved secondary structures with pseudoknots for given RNA sequence alignments.
- McQFold is a program for MCMC-sampling secondary structures with pseudoknots for given RNA sequences.
-
MCMCSALUT is a program for
joint sampling alignments an mutation parameter estimates for a
given pair of DNA sequences.
It is based on a model allowing insertions and deletions of more than one site at a time in combination several options for the subtitution process. -
MCMCALGN is a program for joint
sampling alignments an mutation parameter estimates for a given pair
of DNA sequences.
It is based on a model for the process of insertions and deletions of single nucleotides that was proposed by
J. Thorne, H. Kishino and J. Felsenstein (1991, J. Mol. Evol. 33).
for geo-referenced clustering: http://www.math.uni-frankfurt.de/~stoch/software/ivhg/index.html