Rose: generating sequence families
Stoye J, Evers D, Meyer F (1998)
BIOINFORMATICS 14(2): 157-163.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Stoye, JensUniBi
;
Evers, Dirk;
Meyer, Folker
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Abstract / Bemerkung
Motivation: We present a new probabilistic model of the evolution of RNA-, DNA-, ol protein-like sequences and a software tool, Rose, that implements this model. Guided by an evolutionary tree, a family of related sequences is created from a common ancestor sequence by insertion, deletion and substitution of characters. During this artificial evolutionary process, the 'true' history is logged and the 'correct' multiple sequence alignment is created simultaneously The model also allows for varying rates of mutation within the sequences, making it possible to establish so-called sequence motifs. Results: The data created by Rose are suitable for the evaluation of methods in multiple sequence alignment computation and the prediction of phylogenetic relationships. It can also be useful when reaching courses in or developing models of sequence evolution and in the study of evolutionary processes.
Erscheinungsjahr
1998
Zeitschriftentitel
BIOINFORMATICS
Band
14
Ausgabe
2
Seite(n)
157-163
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/1625402
Zitieren
Stoye J, Evers D, Meyer F. Rose: generating sequence families. BIOINFORMATICS. 1998;14(2):157-163.
Stoye, J., Evers, D., & Meyer, F. (1998). Rose: generating sequence families. BIOINFORMATICS, 14(2), 157-163. https://doi.org/10.1093/bioinformatics/14.2.157
Stoye, Jens, Evers, Dirk, and Meyer, Folker. 1998. “Rose: generating sequence families”. BIOINFORMATICS 14 (2): 157-163.
Stoye, J., Evers, D., and Meyer, F. (1998). Rose: generating sequence families. BIOINFORMATICS 14, 157-163.
Stoye, J., Evers, D., & Meyer, F., 1998. Rose: generating sequence families. BIOINFORMATICS, 14(2), p 157-163.
J. Stoye, D. Evers, and F. Meyer, “Rose: generating sequence families”, BIOINFORMATICS, vol. 14, 1998, pp. 157-163.
Stoye, J., Evers, D., Meyer, F.: Rose: generating sequence families. BIOINFORMATICS. 14, 157-163 (1998).
Stoye, Jens, Evers, Dirk, and Meyer, Folker. “Rose: generating sequence families”. BIOINFORMATICS 14.2 (1998): 157-163.
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Daten bereitgestellt von European Bioinformatics Institute (EBI)
119 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies.
Gardner PP, Watson RJ, Morgan XC, Draper JL, Finn RD, Morales SE, Stott MB., PeerJ 7(), 2019
PMID: 30631651
Gardner PP, Watson RJ, Morgan XC, Draper JL, Finn RD, Morales SE, Stott MB., PeerJ 7(), 2019
PMID: 30631651
SAliBASE: A Database of Simulated Protein Alignments.
Pervez MT, Shah HA, Babar ME, Naveed N, Shoaib M., Evol Bioinform Online 15(), 2019
PMID: 30733625
Pervez MT, Shah HA, Babar ME, Naveed N, Shoaib M., Evol Bioinform Online 15(), 2019
PMID: 30733625
PVTree: A Sequential Pattern Mining Method for Alignment Independent Phylogeny Reconstruction.
Kang Y, Yang X, Lin J, Ye K., Genes (Basel) 10(2), 2019
PMID: 30678245
Kang Y, Yang X, Lin J, Ye K., Genes (Basel) 10(2), 2019
PMID: 30678245
The Evolutionary Traceability of a Protein.
Jain A, Perisa D, Fliedner F, von Haeseler A, Ebersberger I., Genome Biol Evol 11(2), 2019
PMID: 30649284
Jain A, Perisa D, Fliedner F, von Haeseler A, Ebersberger I., Genome Biol Evol 11(2), 2019
PMID: 30649284
A Molecular Portrait of De Novo Genes in Yeasts.
Vakirlis N, Hebert AS, Opulente DA, Achaz G, Hittinger CT, Fischer G, Coon JJ, Lafontaine I., Mol Biol Evol 35(3), 2018
PMID: 29220506
Vakirlis N, Hebert AS, Opulente DA, Achaz G, Hittinger CT, Fischer G, Coon JJ, Lafontaine I., Mol Biol Evol 35(3), 2018
PMID: 29220506
Correlated Selection on Amino Acid Deletion and Replacement in Mammalian Protein Sequences.
Zheng Y, Graur D, Azevedo RBR., J Mol Evol 86(6), 2018
PMID: 29955898
Zheng Y, Graur D, Azevedo RBR., J Mol Evol 86(6), 2018
PMID: 29955898
Toward Reducing Phylostratigraphic Errors and Biases.
Moyers BA, Zhang J., Genome Biol Evol 10(8), 2018
PMID: 30060201
Moyers BA, Zhang J., Genome Biol Evol 10(8), 2018
PMID: 30060201
Computational determination of gene age and characterization of evolutionary dynamics in human.
Yin H, Li M, Xia L, He C, Zhang Z., Brief Bioinform (), 2018
PMID: 30184145
Yin H, Li M, Xia L, He C, Zhang Z., Brief Bioinform (), 2018
PMID: 30184145
PanDelos: a dictionary-based method for pan-genome content discovery.
Bonnici V, Giugno R, Manca V., BMC Bioinformatics 19(suppl 15), 2018
PMID: 30497358
Bonnici V, Giugno R, Manca V., BMC Bioinformatics 19(suppl 15), 2018
PMID: 30497358
A Modified Multiple Alignment Fast Fourier Transform with Higher Efficiency.
Zheng W, Li K, Li K, So HC., IEEE/ACM Trans Comput Biol Bioinform 14(3), 2017
PMID: 26890922
Zheng W, Li K, Li K, So HC., IEEE/ACM Trans Comput Biol Bioinform 14(3), 2017
PMID: 26890922
Inferring Rates and Length-Distributions of Indels Using Approximate Bayesian Computation.
Levy Karin E, Shkedy D, Ashkenazy H, Cartwright RA, Pupko T., Genome Biol Evol 9(5), 2017
PMID: 28453624
Levy Karin E, Shkedy D, Ashkenazy H, Cartwright RA, Pupko T., Genome Biol Evol 9(5), 2017
PMID: 28453624
Further Simulations and Analyses Demonstrate Open Problems of Phylostratigraphy.
Moyers BA, Zhang J., Genome Biol Evol 9(6), 2017
PMID: 28637261
Moyers BA, Zhang J., Genome Biol Evol 9(6), 2017
PMID: 28637261
SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm.
Ashkenazy H, Levy Karin E, Mertens Z, Cartwright RA, Pupko T., Nucleic Acids Res 45(w1), 2017
PMID: 28460062
Ashkenazy H, Levy Karin E, Mertens Z, Cartwright RA, Pupko T., Nucleic Acids Res 45(w1), 2017
PMID: 28460062
Multiple sequence alignment modeling: methods and applications.
Chatzou M, Magis C, Chang JM, Kemena C, Bussotti G, Erb I, Notredame C., Brief Bioinform 17(6), 2016
PMID: 26615024
Chatzou M, Magis C, Chang JM, Kemena C, Bussotti G, Erb I, Notredame C., Brief Bioinform 17(6), 2016
PMID: 26615024
An Integrated Perspective on Phylogenetic Workflows.
Guang A, Zapata F, Howison M, Lawrence CE, Dunn CW., Trends Ecol Evol 31(2), 2016
PMID: 26775796
Guang A, Zapata F, Howison M, Lawrence CE, Dunn CW., Trends Ecol Evol 31(2), 2016
PMID: 26775796
Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution.
Moyers BA, Zhang J., Mol Biol Evol 33(5), 2016
PMID: 26758516
Moyers BA, Zhang J., Mol Biol Evol 33(5), 2016
PMID: 26758516
An evaluation of the accuracy and speed of metagenome analysis tools.
Lindgreen S, Adair KL, Gardner PP., Sci Rep 6(), 2016
PMID: 26778510
Lindgreen S, Adair KL, Gardner PP., Sci Rep 6(), 2016
PMID: 26778510
Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi.
Okagaki LH, Sailsbery JK, Eyre AW, Dean RA., BMC Genomics 17(), 2016
PMID: 26911875
Okagaki LH, Sailsbery JK, Eyre AW, Dean RA., BMC Genomics 17(), 2016
PMID: 26911875
MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation.
Koslicki D, Falush D., mSystems 1(3), 2016
PMID: 27822531
Koslicki D, Falush D., mSystems 1(3), 2016
PMID: 27822531
Fast comparison of genomic and meta-genomic reads with alignment-free measures based on quality values.
Comin M, Schimd M., BMC Med Genomics 9 Suppl 1(), 2016
PMID: 27535823
Comin M, Schimd M., BMC Med Genomics 9 Suppl 1(), 2016
PMID: 27535823
Scaling statistical multiple sequence alignment to large datasets.
Nute M, Warnow T., BMC Genomics 17(suppl 10), 2016
PMID: 28185555
Nute M, Warnow T., BMC Genomics 17(suppl 10), 2016
PMID: 28185555
Phylostratigraphic bias creates spurious patterns of genome evolution.
Moyers BA, Zhang J., Mol Biol Evol 32(1), 2015
PMID: 25312911
Moyers BA, Zhang J., Mol Biol Evol 32(1), 2015
PMID: 25312911
Genetic data simulators and their applications: an overview.
Peng B, Chen HS, Mechanic LE, Racine B, Clarke J, Gillanders E, Feuer EJ., Genet Epidemiol 39(1), 2015
PMID: 25504286
Peng B, Chen HS, Mechanic LE, Racine B, Clarke J, Gillanders E, Feuer EJ., Genet Epidemiol 39(1), 2015
PMID: 25504286
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.
Mirarab S, Nguyen N, Guo S, Wang LS, Kim J, Warnow T., J Comput Biol 22(5), 2015
PMID: 25549288
Mirarab S, Nguyen N, Guo S, Wang LS, Kim J, Warnow T., J Comput Biol 22(5), 2015
PMID: 25549288
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.
Sela I, Ashkenazy H, Katoh K, Pupko T., Nucleic Acids Res 43(w1), 2015
PMID: 25883146
Sela I, Ashkenazy H, Katoh K, Pupko T., Nucleic Acids Res 43(w1), 2015
PMID: 25883146
Ultra-large alignments using phylogeny-aware profiles.
Nguyen NP, Mirarab S, Kumar K, Warnow T., Genome Biol 16(), 2015
PMID: 26076734
Nguyen NP, Mirarab S, Kumar K, Warnow T., Genome Biol 16(), 2015
PMID: 26076734
An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data.
Fan H, Ives AR, Surget-Groba Y, Cannon CH., BMC Genomics 16(), 2015
PMID: 26169061
Fan H, Ives AR, Surget-Groba Y, Cannon CH., BMC Genomics 16(), 2015
PMID: 26169061
Multiple Sequence Alignment with Hidden Markov Models Learned by Random Drift Particle Swarm Optimization.
Sun J, Palade V, Wu X, Fang W., IEEE/ACM Trans Comput Biol Bioinform 11(1), 2014
PMID: 26355522
Sun J, Palade V, Wu X, Fang W., IEEE/ACM Trans Comput Biol Bioinform 11(1), 2014
PMID: 26355522
QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors.
Gudyś A, Deorowicz S., PLoS One 9(2), 2014
PMID: 24586435
Gudyś A, Deorowicz S., PLoS One 9(2), 2014
PMID: 24586435
TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction.
Chang JM, Di Tommaso P, Notredame C., Mol Biol Evol 31(6), 2014
PMID: 24694831
Chang JM, Di Tommaso P, Notredame C., Mol Biol Evol 31(6), 2014
PMID: 24694831
Fast alignment-free sequence comparison using spaced-word frequencies.
Leimeister CA, Boden M, Horwege S, Lindner S, Morgenstern B., Bioinformatics 30(14), 2014
PMID: 24700317
Leimeister CA, Boden M, Horwege S, Lindner S, Morgenstern B., Bioinformatics 30(14), 2014
PMID: 24700317
πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios.
Bielejec F, Lemey P, Carvalho LM, Baele G, Rambaut A, Suchard MA., BMC Bioinformatics 15(), 2014
PMID: 24885610
Bielejec F, Lemey P, Carvalho LM, Baele G, Rambaut A, Suchard MA., BMC Bioinformatics 15(), 2014
PMID: 24885610
Kmacs: the k-mismatch average common substring approach to alignment-free sequence comparison.
Leimeister CA, Morgenstern B., Bioinformatics 30(14), 2014
PMID: 24828656
Leimeister CA, Morgenstern B., Bioinformatics 30(14), 2014
PMID: 24828656
ASTRAL: genome-scale coalescent-based species tree estimation.
Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T., Bioinformatics 30(17), 2014
PMID: 25161245
Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T., Bioinformatics 30(17), 2014
PMID: 25161245
Indel reliability in indel-based phylogenetic inference.
Ashkenazy H, Cohen O, Pupko T, Huchon D., Genome Biol Evol 6(12), 2014
PMID: 25409663
Ashkenazy H, Cohen O, Pupko T, Huchon D., Genome Biol Evol 6(12), 2014
PMID: 25409663
Evaluating the accuracy and efficiency of multiple sequence alignment methods.
Pervez MT, Babar ME, Nadeem A, Aslam M, Awan AR, Aslam N, Hussain T, Naveed N, Qadri S, Waheed U, Shoaib M., Evol Bioinform Online 10(), 2014
PMID: 25574120
Pervez MT, Babar ME, Nadeem A, Aslam M, Awan AR, Aslam N, Hussain T, Naveed N, Qadri S, Waheed U, Shoaib M., Evol Bioinform Online 10(), 2014
PMID: 25574120
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Bakış Y, Otu HH, Taşçı N, Meydan C, Bilgin N, Yüzbaşıoğlu S, Sezerman OU., BMC Bioinformatics 14(), 2013
PMID: 23323678
Bakış Y, Otu HH, Taşçı N, Meydan C, Bilgin N, Yüzbaşıoğlu S, Sezerman OU., BMC Bioinformatics 14(), 2013
PMID: 23323678
A data parallel strategy for aligning multiple biological sequences on multi-core computers.
Zhu X, Li K, Salah A., Comput Biol Med 43(4), 2013
PMID: 23414778
Zhu X, Li K, Salah A., Comput Biol Med 43(4), 2013
PMID: 23414778
GenPhyloData: realistic simulation of gene family evolution.
Sjöstrand J, Arvestad L, Lagergren J, Sennblad B., BMC Bioinformatics 14(), 2013
PMID: 23803001
Sjöstrand J, Arvestad L, Lagergren J, Sennblad B., BMC Bioinformatics 14(), 2013
PMID: 23803001
SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.
Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, Linder CR., Syst Biol 61(1), 2012
PMID: 22139466
Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, Linder CR., Syst Biol 61(1), 2012
PMID: 22139466
ALF--a simulation framework for genome evolution.
Dalquen DA, Anisimova M, Gonnet GH, Dessimoz C., Mol Biol Evol 29(4), 2012
PMID: 22160766
Dalquen DA, Anisimova M, Gonnet GH, Dessimoz C., Mol Biol Evol 29(4), 2012
PMID: 22160766
Accounting for alignment uncertainty in phylogenomics.
Wu M, Chatterji S, Eisen JA., PLoS One 7(1), 2012
PMID: 22272325
Wu M, Chatterji S, Eisen JA., PLoS One 7(1), 2012
PMID: 22272325
REvolver: modeling sequence evolution under domain constraints.
Koestler T, von Haeseler A, Ebersberger I., Mol Biol Evol 29(9), 2012
PMID: 22383532
Koestler T, von Haeseler A, Ebersberger I., Mol Biol Evol 29(9), 2012
PMID: 22383532
PHYRN: a robust method for phylogenetic analysis of highly divergent sequences.
Bhardwaj G, Ko KD, Hong Y, Zhang Z, Ho NL, Chintapalli SV, Kline LA, Gotlin M, Hartranft DN, Patterson ME, Dave F, Smith EJ, Holmes EC, Patterson RL, van Rossum DB., PLoS One 7(4), 2012
PMID: 22514627
Bhardwaj G, Ko KD, Hong Y, Zhang Z, Ho NL, Chintapalli SV, Kline LA, Gotlin M, Hartranft DN, Patterson ME, Dave F, Smith EJ, Holmes EC, Patterson RL, van Rossum DB., PLoS One 7(4), 2012
PMID: 22514627
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Capella-Gutiérrez S, Marcet-Houben M, Gabaldón T., BMC Biol 10(), 2012
PMID: 22651672
Capella-Gutiérrez S, Marcet-Houben M, Gabaldón T., BMC Biol 10(), 2012
PMID: 22651672
Simulation of molecular data under diverse evolutionary scenarios.
Arenas M., PLoS Comput Biol 8(5), 2012
PMID: 22693434
Arenas M., PLoS Comput Biol 8(5), 2012
PMID: 22693434
GenNon-h: generating multiple sequence alignments on nonhomogeneous phylogenetic trees.
Kedzierska AM, Casanellas M., BMC Bioinformatics 13(), 2012
PMID: 22928840
Kedzierska AM, Casanellas M., BMC Bioinformatics 13(), 2012
PMID: 22928840
Towards a practical O(nlogn) phylogeny algorithm.
Truszkowski J, Hao Y, Brown DG., Algorithms Mol Biol 7(1), 2012
PMID: 23181935
Truszkowski J, Hao Y, Brown DG., Algorithms Mol Biol 7(1), 2012
PMID: 23181935
Evaluation of methods for detecting conversion events in gene clusters.
Song G, Hsu CH, Riemer C, Miller W., BMC Bioinformatics 12 Suppl 1(), 2011
PMID: 21342577
Song G, Hsu CH, Riemer C, Miller W., BMC Bioinformatics 12 Suppl 1(), 2011
PMID: 21342577
SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation.
Anderson CL, Strope CL, Moriyama EN., BMC Bioinformatics 12(), 2011
PMID: 21600033
Anderson CL, Strope CL, Moriyama EN., BMC Bioinformatics 12(), 2011
PMID: 21600033
The impact of multiple protein sequence alignment on phylogenetic estimation.
Wang LS, Leebens-Mack J, Kerr Wall P, Beckmann K, dePamphilis CW, Warnow T., IEEE/ACM Trans Comput Biol Bioinform 8(4), 2011
PMID: 21566256
Wang LS, Leebens-Mack J, Kerr Wall P, Beckmann K, dePamphilis CW, Warnow T., IEEE/ACM Trans Comput Biol Bioinform 8(4), 2011
PMID: 21566256
Array Comparative Genomic Hybridizations: assessing the ability to recapture evolutionary relationships using an in silico approach.
Gilbert LB, Chae L, Kasuga T, Taylor JW., BMC Genomics 12(), 2011
PMID: 21936922
Gilbert LB, Chae L, Kasuga T, Taylor JW., BMC Genomics 12(), 2011
PMID: 21936922
Fast and accurate methods for phylogenomic analyses.
Yang J, Warnow T., BMC Bioinformatics 12 Suppl 9(), 2011
PMID: 22152123
Yang J, Warnow T., BMC Bioinformatics 12 Suppl 9(), 2011
PMID: 22152123
HGT-Gen: a tool for generating a phylogenetic tree with horizontal gene transfer.
Horiike T, Miyata D, Tateno Y, Minai R., Bioinformation 7(5), 2011
PMID: 22125388
Horiike T, Miyata D, Tateno Y, Minai R., Bioinformation 7(5), 2011
PMID: 22125388
Towards realistic benchmarks for multiple alignments of non-coding sequences.
Kim J, Sinha S., BMC Bioinformatics 11(), 2010
PMID: 20102627
Kim J, Sinha S., BMC Bioinformatics 11(), 2010
PMID: 20102627
A min-cut algorithm for the consistency problem in multiple sequence alignment.
Corel E, Pitschi F, Morgenstern B., Bioinformatics 26(8), 2010
PMID: 20189940
Corel E, Pitschi F, Morgenstern B., Bioinformatics 26(8), 2010
PMID: 20189940
An alignment confidence score capturing robustness to guide tree uncertainty.
Penn O, Privman E, Landan G, Graur D, Pupko T., Mol Biol Evol 27(8), 2010
PMID: 20207713
Penn O, Privman E, Landan G, Graur D, Pupko T., Mol Biol Evol 27(8), 2010
PMID: 20207713
FastTree 2--approximately maximum-likelihood trees for large alignments.
Price MN, Dehal PS, Arkin AP., PLoS One 5(3), 2010
PMID: 20224823
Price MN, Dehal PS, Arkin AP., PLoS One 5(3), 2010
PMID: 20224823
PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences.
Sahraeian SM, Yoon BJ., Nucleic Acids Res 38(15), 2010
PMID: 20413579
Sahraeian SM, Yoon BJ., Nucleic Acids Res 38(15), 2010
PMID: 20413579
GUIDANCE: a web server for assessing alignment confidence scores.
Penn O, Privman E, Ashkenazy H, Landan G, Graur D, Pupko T., Nucleic Acids Res 38(web server issue), 2010
PMID: 20497997
Penn O, Privman E, Ashkenazy H, Landan G, Graur D, Pupko T., Nucleic Acids Res 38(web server issue), 2010
PMID: 20497997
The construction and use of log-odds substitution scores for multiple sequence alignment.
Altschul SF, Wootton JC, Zaslavsky E, Yu YK., PLoS Comput Biol 6(7), 2010
PMID: 20657661
Altschul SF, Wootton JC, Zaslavsky E, Yu YK., PLoS Comput Biol 6(7), 2010
PMID: 20657661
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment.
Aniba MR, Poch O, Thompson JD., Nucleic Acids Res 38(21), 2010
PMID: 20639539
Aniba MR, Poch O, Thompson JD., Nucleic Acids Res 38(21), 2010
PMID: 20639539
Characterization of pairwise and multiple sequence alignment errors.
Landan G, Graur D., Gene 441(1-2), 2009
PMID: 18614299
Landan G, Graur D., Gene 441(1-2), 2009
PMID: 18614299
Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features.
Lassmann T, Frings O, Sonnhammer EL., Nucleic Acids Res 37(3), 2009
PMID: 19103665
Lassmann T, Frings O, Sonnhammer EL., Nucleic Acids Res 37(3), 2009
PMID: 19103665
Barking up the wrong treelength: the impact of gap penalty on alignment and tree accuracy.
Liu K, Nelesen S, Raghavan S, Linder CR, Warnow T., IEEE/ACM Trans Comput Biol Bioinform 6(1), 2009
PMID: 19179695
Liu K, Nelesen S, Raghavan S, Linder CR, Warnow T., IEEE/ACM Trans Comput Biol Bioinform 6(1), 2009
PMID: 19179695
A hierarchical model for incomplete alignments in phylogenetic inference.
Cheng F, Hartmann S, Gupta M, Ibrahim JG, Vision TJ., Bioinformatics 25(5), 2009
PMID: 19147663
Cheng F, Hartmann S, Gupta M, Ibrahim JG, Vision TJ., Bioinformatics 25(5), 2009
PMID: 19147663
Simultaneous phylogeny reconstruction and multiple sequence alignment.
Yue F, Shi J, Tang J., BMC Bioinformatics 10 Suppl 1(), 2009
PMID: 19208110
Yue F, Shi J, Tang J., BMC Bioinformatics 10 Suppl 1(), 2009
PMID: 19208110
The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome.
Marcet-Houben M, Gabaldón T., PLoS One 4(2), 2009
PMID: 19190756
Marcet-Houben M, Gabaldón T., PLoS One 4(2), 2009
PMID: 19190756
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix.
Price MN, Dehal PS, Arkin AP., Mol Biol Evol 26(7), 2009
PMID: 19377059
Price MN, Dehal PS, Arkin AP., Mol Biol Evol 26(7), 2009
PMID: 19377059
INDELible: a flexible simulator of biological sequence evolution.
Fletcher W, Yang Z., Mol Biol Evol 26(8), 2009
PMID: 19423664
Fletcher W, Yang Z., Mol Biol Evol 26(8), 2009
PMID: 19423664
Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees.
Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T., Science 324(5934), 2009
PMID: 19541996
Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T., Science 324(5934), 2009
PMID: 19541996
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T., Bioinformatics 25(15), 2009
PMID: 19505945
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T., Bioinformatics 25(15), 2009
PMID: 19505945
Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0.
Strope CL, Abel K, Scott SD, Moriyama EN., Mol Biol Evol 26(11), 2009
PMID: 19651852
Strope CL, Abel K, Scott SD, Moriyama EN., Mol Biol Evol 26(11), 2009
PMID: 19651852
Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion.
Birin H, Gal-Or Z, Elias I, Tuller T., Bioinformatics 24(6), 2008
PMID: 18203769
Birin H, Gal-Or Z, Elias I, Tuller T., Bioinformatics 24(6), 2008
PMID: 18203769
Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?
Hartmann S, Vision TJ., BMC Evol Biol 8(), 2008
PMID: 18366758
Hartmann S, Vision TJ., BMC Evol Biol 8(), 2008
PMID: 18366758
Reconstruction of genuine pair-wise sequence alignment.
Polyanovsky V, Roytberg MA, Tumanyan VG., J Comput Biol 15(4), 2008
PMID: 18435572
Polyanovsky V, Roytberg MA, Tumanyan VG., J Comput Biol 15(4), 2008
PMID: 18435572
DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment.
Subramanian AR, Kaufmann M, Morgenstern B., Algorithms Mol Biol 3(), 2008
PMID: 18505568
Subramanian AR, Kaufmann M, Morgenstern B., Algorithms Mol Biol 3(), 2008
PMID: 18505568
Grammar-based distance in progressive multiple sequence alignment.
Russell DJ, Otu HH, Sayood K., BMC Bioinformatics 9(), 2008
PMID: 18616828
Russell DJ, Otu HH, Sayood K., BMC Bioinformatics 9(), 2008
PMID: 18616828
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Soria-Carrasco V, Castresana J., Mol Biol Evol 25(11), 2008
PMID: 18701430
Soria-Carrasco V, Castresana J., Mol Biol Evol 25(11), 2008
PMID: 18701430
Probabilistic phylogenetic inference with insertions and deletions.
Rivas E, Eddy SR., PLoS Comput Biol 4(9), 2008
PMID: 18787703
Rivas E, Eddy SR., PLoS Comput Biol 4(9), 2008
PMID: 18787703
Tools for simulating evolution of aligned genomic regions with integrated parameter estimation.
Varadarajan A, Bradley RK, Holmes IH., Genome Biol 9(10), 2008
PMID: 18840304
Varadarajan A, Bradley RK, Holmes IH., Genome Biol 9(10), 2008
PMID: 18840304
Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment.
Kim J, Sinha S., Bioinformatics 23(3), 2007
PMID: 17110370
Kim J, Sinha S., Bioinformatics 23(3), 2007
PMID: 17110370
Simultaneous alignment and annotation of cis-regulatory regions.
Bais AS, Grossmann S, Vingron M., Bioinformatics 23(2), 2007
PMID: 17237103
Bais AS, Grossmann S, Vingron M., Bioinformatics 23(2), 2007
PMID: 17237103
A simulation test bed for hypotheses of genome evolution.
Beiko RG, Charlebois RL., Bioinformatics 23(7), 2007
PMID: 17267425
Beiko RG, Charlebois RL., Bioinformatics 23(7), 2007
PMID: 17267425
MySSP: non-stationary evolutionary sequence simulation, including indels.
Rosenberg MS., Evol Bioinform Online 1(), 2007
PMID: 19325855
Rosenberg MS., Evol Bioinform Online 1(), 2007
PMID: 19325855
COBALT: constraint-based alignment tool for multiple protein sequences.
Papadopoulos JS, Agarwala R., Bioinformatics 23(9), 2007
PMID: 17332019
Papadopoulos JS, Agarwala R., Bioinformatics 23(9), 2007
PMID: 17332019
Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP*.
Ogden TH, Rosenberg MS., Syst Biol 56(2), 2007
PMID: 17454974
Ogden TH, Rosenberg MS., Syst Biol 56(2), 2007
PMID: 17454974
On homology searches by protein Blast and the characterization of the age of genes.
Albà MM, Castresana J., BMC Evol Biol 7(), 2007
PMID: 17408474
Albà MM, Castresana J., BMC Evol Biol 7(), 2007
PMID: 17408474
The relative performance of indel-coding methods in simulations.
Simmons MP, Müller K, Norton AP., Mol Phylogenet Evol 44(2), 2007
PMID: 17512758
Simmons MP, Müller K, Norton AP., Mol Phylogenet Evol 44(2), 2007
PMID: 17512758
Automatic extraction of reliable regions from multiple sequence alignments.
Lassmann T, Sonnhammer EL., BMC Bioinformatics 8 Suppl 5(), 2007
PMID: 17570868
Lassmann T, Sonnhammer EL., BMC Bioinformatics 8 Suppl 5(), 2007
PMID: 17570868
Progressive multiple sequence alignments from triplets.
Kruspe M, Stadler PF., BMC Bioinformatics 8(), 2007
PMID: 17631683
Kruspe M, Stadler PF., BMC Bioinformatics 8(), 2007
PMID: 17631683
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.
Talavera G, Castresana J., Syst Biol 56(4), 2007
PMID: 17654362
Talavera G, Castresana J., Syst Biol 56(4), 2007
PMID: 17654362
Incorporating evolution of transcription factor binding sites into annotated alignments.
Bais AS, Grossmann S, Vingron M., J Biosci 32(5), 2007
PMID: 17914226
Bais AS, Grossmann S, Vingron M., J Biosci 32(5), 2007
PMID: 17914226
Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites.
Moses AM, Liku ME, Li JJ, Durbin R., Proc Natl Acad Sci U S A 104(45), 2007
PMID: 17978194
Moses AM, Liku ME, Li JJ, Durbin R., Proc Natl Acad Sci U S A 104(45), 2007
PMID: 17978194
Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes.
Rasmussen MD, Kellis M., Genome Res 17(12), 2007
PMID: 17989260
Rasmussen MD, Kellis M., Genome Res 17(12), 2007
PMID: 17989260
In silico sequence evolution with site-specific interactions along phylogenetic trees.
Gesell T, von Haeseler A., Bioinformatics 22(6), 2006
PMID: 16332711
Gesell T, von Haeseler A., Bioinformatics 22(6), 2006
PMID: 16332711
On conditioned reconstruction, gene content data, and the recovery of fusion genomes.
Bailey CD, Fain MG, Houde P., Mol Phylogenet Evol 39(1), 2006
PMID: 16414287
Bailey CD, Fain MG, Houde P., Mol Phylogenet Evol 39(1), 2006
PMID: 16414287
Family specific rates of protein evolution.
Luz H, Vingron M., Bioinformatics 22(10), 2006
PMID: 16510497
Luz H, Vingron M., Bioinformatics 22(10), 2006
PMID: 16510497
Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method.
Evans J, Sheneman L, Foster J., J Mol Evol 62(6), 2006
PMID: 16752216
Evans J, Sheneman L, Foster J., J Mol Evol 62(6), 2006
PMID: 16752216
Probalign: multiple sequence alignment using partition function posterior probabilities.
Roshan U, Livesay DR., Bioinformatics 22(22), 2006
PMID: 16954142
Roshan U, Livesay DR., Bioinformatics 22(22), 2006
PMID: 16954142
The accuracy of several multiple sequence alignment programs for proteins.
Nuin PA, Wang Z, Tillier ER., BMC Bioinformatics 7(), 2006
PMID: 17062146
Nuin PA, Wang Z, Tillier ER., BMC Bioinformatics 7(), 2006
PMID: 17062146
Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences.
Hall BG., Mol Biol Evol 22(3), 2005
PMID: 15590907
Hall BG., Mol Biol Evol 22(3), 2005
PMID: 15590907
Impact of taxon sampling on the estimation of rates of evolution at sites.
Blouin C, Butt D, Roger AJ., Mol Biol Evol 22(3), 2005
PMID: 15590908
Blouin C, Butt D, Roger AJ., Mol Biol Evol 22(3), 2005
PMID: 15590908
DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment.
Subramanian AR, Weyer-Menkhoff J, Kaufmann M, Morgenstern B., BMC Bioinformatics 6(), 2005
PMID: 15784139
Subramanian AR, Weyer-Menkhoff J, Kaufmann M, Morgenstern B., BMC Bioinformatics 6(), 2005
PMID: 15784139
Scoredist: a simple and robust protein sequence distance estimator.
Sonnhammer EL, Hollich V., BMC Bioinformatics 6(), 2005
PMID: 15857510
Sonnhammer EL, Hollich V., BMC Bioinformatics 6(), 2005
PMID: 15857510
Multiple sequence alignments.
Wallace IM, Blackshields G, Higgins DG., Curr Opin Struct Biol 15(3), 2005
PMID: 15963889
Wallace IM, Blackshields G, Higgins DG., Curr Opin Struct Biol 15(3), 2005
PMID: 15963889
Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction.
Hollich V, Milchert L, Arvestad L, Sonnhammer EL., Mol Biol Evol 22(11), 2005
PMID: 16049194
Hollich V, Milchert L, Arvestad L, Sonnhammer EL., Mol Biol Evol 22(11), 2005
PMID: 16049194
Genomic multiple sequence alignments: refinement using a genetic algorithm.
Wang C, Lefkowitz EJ., BMC Bioinformatics 6(), 2005
PMID: 16086841
Wang C, Lefkowitz EJ., BMC Bioinformatics 6(), 2005
PMID: 16086841
SIMPROT: using an empirically determined indel distribution in simulations of protein evolution.
Pang A, Smith AD, Nuin PA, Tillier ER., BMC Bioinformatics 6(), 2005
PMID: 16188037
Pang A, Smith AD, Nuin PA, Tillier ER., BMC Bioinformatics 6(), 2005
PMID: 16188037
Ancestral sequence alignment under optimal conditions.
Hudek AK, Brown DG., BMC Bioinformatics 6(), 2005
PMID: 16293191
Hudek AK, Brown DG., BMC Bioinformatics 6(), 2005
PMID: 16293191
Kalign--an accurate and fast multiple sequence alignment algorithm.
Lassmann T, Sonnhammer EL., BMC Bioinformatics 6(), 2005
PMID: 16343337
Lassmann T, Sonnhammer EL., BMC Bioinformatics 6(), 2005
PMID: 16343337
ThurGood: evaluating assembly-to-assembly mapping.
Shatkay H, Miller J, Mobarry C, Flanigan M, Yooseph S, Sutton G., J Comput Biol 11(5), 2004
PMID: 15700403
Shatkay H, Miller J, Mobarry C, Flanigan M, Yooseph S, Sutton G., J Comput Biol 11(5), 2004
PMID: 15700403
Benchmarking tools for the alignment of functional noncoding DNA.
Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB., BMC Bioinformatics 5(), 2004
PMID: 14736341
Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB., BMC Bioinformatics 5(), 2004
PMID: 14736341
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Edgar RC., Nucleic Acids Res 32(5), 2004
PMID: 15034147
Edgar RC., Nucleic Acids Res 32(5), 2004
PMID: 15034147
Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta).
Müller T, Rahmann S, Dandekar T, Wolf M., BMC Evol Biol 4(), 2004
PMID: 15222898
Müller T, Rahmann S, Dandekar T, Wolf M., BMC Evol Biol 4(), 2004
PMID: 15222898
Fast and sensitive multiple alignment of large genomic sequences.
Brudno M, Chapman M, Göttgens B, Batzoglou S, Morgenstern B., BMC Bioinformatics 4(), 2003
PMID: 14693042
Brudno M, Chapman M, Göttgens B, Batzoglou S, Morgenstern B., BMC Bioinformatics 4(), 2003
PMID: 14693042
Algorithms for phylogenetic footprinting.
Blanchette M, Schwikowski B, Tompa M., J Comput Biol 9(2), 2002
PMID: 12015878
Blanchette M, Schwikowski B, Tompa M., J Comput Biol 9(2), 2002
PMID: 12015878
Quality assessment of multiple alignment programs.
Lassmann T, Sonnhammer EL., FEBS Lett 529(1), 2002
PMID: 12354624
Lassmann T, Sonnhammer EL., FEBS Lett 529(1), 2002
PMID: 12354624
References
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