Online citations, reference lists, and bibliographies.
← Back to Search

The Alignment Of Sets Of Sequences And The Construction Of Phyletic Trees: An Integrated Method

P. Hogeweg, B. Hesper
Published 2005 · Biology, Medicine

Cite This
Download PDF
Analyze on Scholarcy
Share
SummaryIn this paper we argue that the alignment of sets of sequences and the construction of phyletic trees cannot be treated separately. The concept of ‘good alignment’ is meaningless without reference to a phyletic tree, and the construction of phyletic trees presupposes alignment of the sequences.We propose an integrated method that generates both an alignment of a set of sequences and a phyletic tree. In this method a putative tree is used to align the sequences and the alignment obtained is used to adjust the tree; this process is iterated. As a demonstration we apply the method to the analysis of the evolution of 5S rRNA sequences in prokaryotes.
This paper references
10.1016/0001-8708(76)90202-4
Some Biological Sequence Metrics
M. Waterman (1976)
Origins ofProkaryotes , Eukaryotes , Mitochondria and Chloroplasts : a perspective is derived from protein and nucleic acid sequence data
PH Sellars (1978)
The phylogeny of prokaryotes.
G. Fox (1980)
10.1016/0022-2836(71)90390-1
Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c 551 .
A. McLachlan (1971)
10.1007/BF02100219
Computer comparison of new and existing criteria for constructing evolutionary trees from sequence data
R. L. Blanken (2005)
10.1007/BF01732010
Phylogenies from amino acid sequences aligned with gaps: The problem of gap weighting
W. Fitch (2005)
10.1016/0010-4825(76)90027-5
Iterative character weighing in numerical taxonomy.
P. Hogeweg (1976)
10.1016/0031-3203(81)90054-6
Oligothetic characterisation of clusters
P. Hogeweg (1981)
10.1007/BF01733210
Comparative biosequence metrics
T. Smith (2005)
Phylogenetic tree
H Kuntzel (1981)
10.1002/9780470122921.CH2
Prediction of the secondary structure of proteins from their amino acid sequence.
P. Y. Chou (1978)
BIOPAT , program system for bioinformatic pattern analysis
P UtrechtHogeweg (1972)
10.1137/0126070
On the Theory and Computation of Evolutionary Distances
P. Sellers (1974)
10.1007/BF01840887
Accuracy of estimated phylogenetic trees from molecular data
Y. Tateno (2005)
10.1016/0022-5193(83)90343-0
Phenetic methods of classification use information that is disregarded by minimum-length methods
A. Cornish-Bowden (1983)
A strategy for
SankoffRJ (1982)
10.1007/BF02300753
Accuracy of estimated phylogenetic trees from molecular data
M. Nei (2006)
A guide to herbarium taxonomy
PW Leenhouts (1968)
Evolutionary change in 5 S RNA secondary structure and a phylogenetic tree of 54 5 S RNA species
LC Klotz (1979)
10.1073/PNAS.76.9.4516
Calculation of evolutionary trees from sequence data.
Lynn C. Klotz (1979)
10.1038/256505a0
5S RNA secondary structure
GEORGE E. Fox (1975)
10.1016/0022-2836(70)90057-4
A general method applicable to the search for similarities in the amino acid sequence of two proteins.
S. B. Needleman (1970)
10.1016/B978-0-12-131200-8.50031-9
A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins
S. B. Needleman (1989)
1976b) Topics in biological pattern analysis
P Hogeweg (1976)
A practical method for calculating
LC Klotz (1981)
BIOPAT, program system
sis (1972)
Accuracy ofestimated phylogenetic trees from molecu / ar data I . Distantly related species
MS Waterman (1982)
10.1016/0022-5193(81)90233-2
A practical method for calculating evolutionary trees from sequence data.
Lynn C. Klotz (1981)
Purposeful phenetics
J McNeill (1978)
Accuracy ofestimated phy
Y Tateno (1982)
10.1093/nar/10.1.421
A strategy for sequence phylogeny research
D. Sankoff (1982)
10.1126/SCIENCE.202030
Origins of prokaryotes, eukaryotes, mitochondria, and chloroplasts.
R. Schwartz (1978)
10.1073/PNAS.76.1.381
Evolutionary change in 5S RNA secondary structure and a phylogenic tree of 54 5S RNA species.
H. Hori (1979)
10.1111/j.1748-1716.1968.tb04201.x
[General method].
T. Horowitz (2000)
10.1093/NAR/9.6.1451
Phylogenetic tree derived from bacterial, cytosol and organelle 5S rRNA sequences.
H. Küntzel (1981)



This paper is referenced by
10.5626/JOK.2016.43.3.289
Malware Family Recommendation using Multiple Sequence Alignment
In Kyeom Cho (2016)
Novel Algorithms and Methodology toHelp Unravel Secrets that NextGeneration Sequencing Data Can Tell
Andrei-Alin Popescu (2015)
10.1109/TKDE.2006.197
Structured Data Extraction from the Web Based on Partial Tree Alignment
Yanhong Zhai (2006)
10.1007/978-981-15-5421-6_36
Multiple Sequence Alignment Algorithm Using Adaptive Evolutionary Clustering
J. Lakhani (2021)
10.11646/zootaxa.3825.1.1
Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria.
J. Padial (2014)
10.1371/journal.pcbi.1002021
The Roots of Bioinformatics in Theoretical Biology
P. Hogeweg (2011)
Alinhamento múltiplo de proteínas utilizando algoritmos genéticos
Sérgio Jeferson Rafael Ordine (2015)
Methodology for predicting semantic annotations of protein sequences by feature extraction derived of statistical contact potentials and continuous wavelet transform
Arango Argoty (2019)
10.1128/JB.00121-20
Molecular Design of a Signaling System Influences Noise in Protein Abundance under Acid Stress in Different Gammaproteobacteria
Sophie Brameyer (2020)
Alinhamento múltiplo progressivo de sequências de proteínas
Maria Angélica Souza (2010)
10.1038/s41598-017-09499-1
Bacterial Foraging Optimization –Genetic Algorithm for Multiple Sequence Alignment with Multi-Objectives
P. Manikandan (2017)
10.1038/msb.2011.75
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
F. Sievers (2011)
10.5220/0003789202260233
Improvements to a Multiple Protein Sequence Alignment Tool
André Atanasio M. Almeida (2012)
10.5120/1761-2411
Automation of DNA Finger Printing for Precise Pattern Identification using Neural-fuzzy Mapping approach
A. Pushpalatha (2011)
Analysis of multiple protein sequence alignments and phylogenetic trees in the context of phylogenomics studies
Capella Gutiérrez (2012)
Computational pan-genomics: algorithms and applications
Alan M. Cleary (2018)
10.1007/s00442-005-0193-2
Piriformospora indica and Sebacina vermifera increase growth performance at the expense of herbivore resistance in Nicotiana attenuata
O. Barazani (2005)
10.1093/bioinformatics/bti582
SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures
Hongyi Zhou (2005)
10.1093/sysbio/syp009
Why would phylogeneticists ignore computerized sequence alignment?
D. Morrison (2009)
The impact of guide trees in large-scale protein multiple sequence alignments
K. Boyce (2016)
10.1109/EIT.2008.4554299
A new heuristic for multiple sequence alignment
A. Agrawal (2008)
10.1016/B978-0-444-53632-7.01108-4
6.07 – Phylogenetic Analyses
Punto Bawono (2014)
10.1016/j.jbi.2005.11.005
Homology assessment and molecular sequence alignment
A. Phillips (2006)
10.1071/SB06020
Multiple sequence alignment for phylogenetic purposes
D. Morrison (2006)
Visual Search and Analysis in Molecular Biology
M. Hess (2018)
10.1002/9780470741894.CH1
The Basics of Protein Sequence Analysis
Katarzyna Kamińska (2008)
10.1186/s12859-015-0696-8
MultiSETTER: web server for multiple RNA structure comparison
P. Cech (2015)
An Associative Model of Word Use a Dissertation Proposal
Scott A. Waterman (1994)
10.1109/CSB.2004.120
MUSCLE: multiple sequence alignment with improved accuracy and speed
R. Edgar (2004)
10.1093/bioinformatics/btz377
Efficient merging of genome profile alignments
A. Hennig (2019)
10.1093/protein/gzw016
ANTICALIgN: visualizing, editing and analyzing combined nucleotide and amino acid sequence alignments for combinatorial protein engineering.
A. Jarasch (2016)
10.1186/1745-6150-8-3
Next-generation phylogenomics
C. Chan (2012)
See more
Semantic Scholar Logo Some data provided by SemanticScholar