The alignment of sets of sequences and the construction of phyletic trees: An integrated method

P. Hogeweg; B. Hesper

doi:10.1007/bf02257378

journal article Jun 01, 1984

The alignment of sets of sequences and the construction of phyletic trees: An integrated method

P. Hogeweg B. Hesper

Journal of Molecular Evolution Vol. 20 No. 2 pp. 175-186 · Springer Science and Business Media LLC

View at Publisher Save 10.1007/bf02257378

Topics

No keywords indexed for this article. Browse by subject →

References

27

[1]

Blanken RL, Klotz LC, Hinnebusch AG (1982) Computer comparison of new and existing criteria for constructing evolutionary trees from sequence data. J Mol Evol 19:9–19 10.1007/bf02100219

[2]

Chou FE, Fasman GD (1978) Prediction of secondary structure of proteins from their amino acid sequence. Adv Enzyol. 47:145–148

[3]

Cornish-Bowden A (1983) Phenetic methods of classification use information discarded by minimum length methods. J Theor Biol 101:317–319 10.1016/0022-5193(83)90343-0

[4]

Dayhoff MO (1976) Atlas of protein structure, vol 5, suppl 2. National Biochemical Research Foundation, Washington, DC

[5]

Fitch WM, Yasunobu KT (1974) Phylogenies from amino acid sequences aligned with gaps: the problem of gap weighting. J Mol Evol 5:1–24 10.1007/bf01732010

[6]

Fox GE, Woese CR (1975) 5S RNA secondary structure. Nature 256:505–507 10.1038/256505a0

[7]

Fox GE, Stackebrandt RB, Hespell RB, Gibson J, Maniloff J, Dyer TA, Wolfe RS, Balch WE, Tanner RS, Magrum LJ, Zablen LB Blakemore R, Gupta R, Bonen L, Lewis BJ, Stahl DA, Luehrsen KR, Chen KN, Woese CR (1980) The phylogeny of prokaryotes. Science 209:457–463 10.1126/science.6771870

[8]

Hogeweg P (1976a) Iterative character weighting in numerical taxonomy. Comput Biol Med 6:166–211 10.1016/0010-4825(76)90027-5

[9]

Hogeweg P (1976b) Topics in biological pattern analysis. Thesis, RU Utrecht

[10]

Hogeweg P, Hesper B (1972) BIOPAT, program system for bioinformatic pattern analysis. Bioinformatica, Utrecht

[11]

Hogeweg P, Hesper B (1981) Oligothetic characterisation of clusters. Pattern Recognition 14:131–136 10.1016/0031-3203(81)90054-6

[12]

Hori H, Osawa S (1979) Evolutionary change in 5S RNA secondary structure and a phylogenetic tree of 54 5S RNA species. Proc Natl Acad Sci USA 16:381–385 10.1073/pnas.76.1.381

[13]

Klotz LC, Blanken RL (1981) A practical method for calculating evolutionary trees from sequence data. J Theor Biol 91:216–272 10.1016/0022-5193(81)90233-2

[14]

Klotz LC, Komar N, Blanken RL, Mitchell RM (1979) Calculation of evolutionary trees from sequence data. Proc Natl Acad Sci USA 76:4516 10.1073/pnas.76.9.4516

[15]

Kuntzel H, Heidrich M, Piechulla B (1981) Phylogenetic tree derived from bacterial, cytosol and organelle 5 S rRNA sequences. Nucleic Acids Res 9:1451–1461 10.1093/nar/9.6.1451

[16]

Leenhouts PW (1968) A guide to herbarium taxonomy. IAPT, Utrecht (Regnum vegetabile, vol 58)

[17]

Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c551

A.D. McLachlan

Journal of Molecular Biology 1971 10.1016/0022-2836(71)90390-1

[18]

McNeill J (1978) Purposeful phenetics. Syst Zool 28:465–482 10.2307/2412561

[19]

A general method applicable to the search for similarities in the amino acid sequence of two proteins

Saul B. Needleman, Christian D. Wunsch

Journal of Molecular Biology 1970 10.1016/0022-2836(70)90057-4

[20]

Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data II. Gene frequency data. J Mol Evol 19:153–170 10.1007/bf02300753

[21]

Sankoff RJ, Cedergren RJ, McKay W (1982) A strategy for sequence phylogeny research. Nucleic Acids Res 10:421–431 10.1093/nar/10.1.421

[22]

Schwartz RM, Dayhoff MO (1978) Origins of Prokaryotes, Eukaryotes, Mitochondria and Chloroplasts: a perspective is derived from protein and nucleic acid sequence data. Science 199:395–403 10.1126/science.202030

[23]

Sellars PH (1974) On the theory and computation of evolutionary distances. SIAM J Appl Math 26:787–793 10.1137/0126070

[24]

Smith TF, Waterman MS, Fitch WM (1981) Comparative biosequence metrics, J Mol Evol 18:38–46 10.1007/bf01733210

[25]

Sneath HA, Sokal RR (1973) Numerical taxonomy. WH Freeman, San Francisco, London

[26]

Tateno Y, Nei M, Tajima F (1982) Accuracy of estimated phylogenetic trees from molecular data I. Distantly related species. J Mol Evol 18:387–404 10.1007/bf01840887

[27]

Waterman MS, Smith TF, Beyer WA (1976) Some biological sequence metrics. Adv Math 20:267–287 10.1016/0001-8708(76)90202-4

Cited By

197

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

Kazutaka Katoh, John Rozewicki · 2017

Briefings in Bioinformatics

Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization

Andres Veidenberg, Alan Medlar · 2015

Molecular Biology and Evolution

Clustal Omega

Fabian Sievers, Desmond G. Higgins · 2014

Current Protocols in Bioinformatics

PRALINE: A Versatile Multiple Sequence Alignment Toolkit

Punto Bawono, Jaap Heringa · 2013

Methods in Molecular Biology™

Next-generation phylogenomics

Cheong Xin Chan, Mark A Ragan · 2013

Biology Direct

PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences

Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon · 2010

Nucleic Acids Research

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

Carsten Kemena, Cedric Notredame · 2009

Bioinformatics

Why Would Phylogeneticists Ignore Computerized Sequence Alignment?

David A. Morrison · 2009

Systematic Biology

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

Benedict Paten, Javier Herrero · 2008

Genome Research

Recent Evolutions of Multiple Sequence Alignment Algorithms

Cedric Notredame · 2007

PLOS Computational Biology

SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures

Hongyi Zhou, Yaoqi Zhou · 2005

Bioinformatics

An algorithm for progressive multiple alignment of sequences with insertions

Ari Löytynoja, Nick Goldman · 2005

Proceedings of the National Academy...

3DCoffee: Combining Protein Sequences and Structures within Multiple Sequence Alignments

Orla O'Sullivan, Karsten Suhre · 2004

Journal of Molecular Biology

Local weighting schemes for protein multiple sequence alignment

Jaap Heringa · 2002

Computers & Chemistry

Multiple Sequence Alignment Using ClustalW and ClustalX

Julie D. Thompson, Toby. J. Gibson · 2002

Current Protocols in Bioinformatics

Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment

Jaap Heringa · 1999

Computers & Chemistry

Multiple sequence alignment: Algorithms and applications

O GOTOH · 1999

Advances in Biophysics

Seventy-five percent accuracy in protein secondary structure prediction

Dmitrij Frishman, Patrick Argos · 1997

Proteins: Structure, Function, and...

A method to recognize distant repeats in protein sequences

Jaap Heringa, Patrick Argos · 1993

Proteins: Structure, Function, and...

Recognition of distantly related protein sequences using conserved motifs and neural networks

Dmitrij Frishman, Patrick Argos · 1992

Journal of Molecular Biology

Metrics

197

Citations

27

References

Details

Published: Jun 01, 1984
Vol/Issue: 20(2)
Pages: 175-186
License: View

Authors

Cite This Article

P. Hogeweg, B. Hesper (1984). The alignment of sets of sequences and the construction of phyletic trees: An integrated method. Journal of Molecular Evolution, 20(2), 175-186. https://doi.org/10.1007/bf02257378

The alignment of sets of sequences and the construction of phyletic trees: An integrated method

You May Also Like