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EBIGroupsGoldman GroupPublications

Goldman Group Publications

The following is a list of publications for the Goldman group.
Click here to request electronic reprint.


2009


Miscellaneous
Huang, G.J., Shifman, S., Valdar, W., Johannesson, M., Yalcin, B., Taylor, M.S., Taylor, J.M., Mott, R., Flint, J. (2009)
High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues.
Genome Research 19, 1133-1140.
citation detail

Miscellaneous
Taylor, M.S., Jordan, G.E., Semple, C.A.M. (2009)
Comparative genomics and mammalian promoter evolution. In: Carninci, P. (Ed.), Cap Analysis Gene Expression (CAGE)
Pan Stanford Publishing, New York, NY, p. 288

Thesis
Pardi, F. (2009)
Algorithms on Phylogenetic Trees
University of Cambridge, Cambridge, p. 200
thesis PDF

Phylogenetic Information
San Mauro, D., Gower, D.J., Massingham, T., Wilkinson, M., Zardoya, R., Cotton, J.A. (2009)
Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1
Syst. Biol. 58, 425-438

Miscellaneous
Semple, C.A.M., Taylor, M.S. (2009)
The structure of change
Science 323, 347-348
citation detail

Phylogenetic Diversity
Minh, B.Q., Pardi, F., Klaere, S., von Haeseler, A. (2009)
Budgeted phylogenetic diversity on circular split systems
IEEE/ACM Transactions on Computational Biology and Bioinformatics 6, 22-29
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Miscellaneous
Bishop, C.J., Aanensen, D.M., Jordan, G.E., Kilian, M., Hanage, W.P., Spratt, B.G. (2009)
Assigning strains to bacterial species via the internet
BMC Biology 7, 3
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Applications
FANTOM consortium and the Riken Omics Science Center, T. (2009)
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
Nature Genetics 41, 553-562
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Alignment
Löytynoja, A., Goldman, N. (2009)
Uniting alignments and trees
Science 324, 1528-1529.
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Phylogenetic Methods
Yang, Z., Nielsen, R., Goldman, N. (2009)
In defense of statistical methods for detecting positive selection
Proc. Natl. Acad. Sci. USA 106, E95
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2008


Phylogenetic Diversity
Faller, B., Pardi, F., Steel, M. (2008)
Distribution of phylogenetic diversity under random extinction.
J. Theor. Biol. 251, 286-296
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Miscellaneous
Goldman, N., Yang, Z. (2008)
Statistical and computational challenges in molecular phylogenetics and evolution
Phil. Trans. R. Soc. Lond. B 363, 3889-3892
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Phylogenetic Methods
Gesell, T., Washietl, S. (2008)
Dinucleotide controlled null models for comparative RNA gene prediction
BMC Bioinformatics 9, 248
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Phylogenetic Methods
Gruber, A.R., Bernhart, S.H., Hofacker, I.L., Washietl, S. (2008)
Strategies for measuring evolutionary conservation of RNA secondary structures
BMC Bioinformatics 9, 122
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Miscellaneous
Huggett, J.F., Taylor, M.S., Kocjan, G., Evans, H.E., Morris-Jones, S., Gant, V., Novak, T., Costello, A.M., Zumla, A., Miller, R.F. (2008)
Development and evaluation of a real-time PCR assay for detection of Pneumocystis jirovecii DNA in bronchoalveolar lavage fluid of HIV-infected patients.
Thorax 63, 154-159.
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Miscellaneous
Jordan, G.E., Piel, W.H. (2008)
PhyloWidget: web-based visualizations for the tree of life
Bioinformatics 24, 1641-1642
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Applications
Ke, X., Taylor, M.S., Cardon, L.R. (2008)
Singleton SNPs in the human genome and implications for genome-wide association studies
European Journal of Human Genetics 16, 506-515
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Alignment
Löytynoja, A., Goldman, N. (2008)
A model of evolution and structure for multiple sequence alignment
Phil. Trans. R. Soc. Lond. B 363, 3913-3919
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Alignment
Löytynoja, A., Goldman, N. (2008)
Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
Science 320, 1632-1635.
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Structure, evolution and HMMS
Madera, M. (2008)
Profile Comparer: a program for scoring and aligning profile hidden Markov models
Bioinformatics 24, 2630-2631.
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Phylogenetic Methods
Massingham, T. (2008)
Detecting the presence and location of selection in proteins
Keith, J.M. (Ed.), Bioinformatics. Humana Press, Totowa, NJ, USA, pp. 311-329.
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Applications
Pain, A., Bohme, U., Berry, A.E., Mungall, K., Finn, R.D., Jackson, A.P., Mourier, T., Mistry, J., Pasini, E.M., Aslett, M.A., ..., Meyer, I.M., ..., authors), t.o., (2008)
The genome of the simian and human malaria parasite Plasmodium knowlesi
Nature 455, 799-803
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Phylogenetic Methods
Taylor, M.S., Massingham, T., Hayashizaki, Y., Carninci, P., Goldman, N., Semple, C.A.M. (2008)
Rapidly evolving human promoter regions
Nature Genetics 40, 1262-1263
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Applications
Tress, M.L., Wesselink, J.-J., Frankish, A., Lopez, G., Goldman, N., Löytynoja, A., Massingham, T., Pardi, F., Whelan, S., Harrow, J., Valencia, A. (2008)
Determination and validation of principal gene products.
Bioinformatics 24, 11-17.
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Applications
Washietl, S., Machné, R., Goldman, N. (2008)
Evolutionary footprints of nucleosome positions in yeast
Trends Gen. 24, 583-587
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Phylogenetic Methods
Whelan, S. (2008)
Inferring trees
Keith, J.M. (Ed.), Bioinformatics. Humana Press, Totowa, NJ, USA, pp. 287-309.
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2007


Phylogenetic Information
Geuten, K., Massingham, T., Darius, P., Smets, E., Goldman, N. (2007)
Experimental design criteria in phylogenetics: where to add taxa
Syst. Biol. 56, 609-622
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Phylogenetic Methods
Bofkin, L., Goldman, N. (2007)
Variation in evolutionary processes at different codon positions
Mol. Biol. Evol. 24, 513-521
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Applications
ENCODE Project Consortium, T. (2007)
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Nature 447, 799-816
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Miscellaneous
Kankainen, M., Löytynoja, A. (2007)
MATLIGN: a motif clustering, comparison and matching tool
BMC Bioinformatics 8, 189
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Models
Kosiol, C., Holmes, I., Goldman, N. (2007)
An empirical codon model for protein sequence evolution
Mol. Biol. Evol. 24, 1464-1479
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Thesis
Kuhn, S. (2007)
Properties of the log-det estimator
Master thesis, University of Cambridge

Applications
Margulies, E.H., Cooper, G.M., Asimenos, G., Thomas, D.J., Dewey, C.N., Siepel, A., Birney, E., Keefe, D., Schwartz, A.S., Hou, M., Taylor, J., Nikolaev, S., Montoya-Burgos, J.I., Loytynoja, A., Whelan, S., Pardi, F., Massingham, T., Brown, J.B., Bickel, P., Holmes, I., Mullikin, J.C., Ureta-Vidal, A., Paten, B., Stone, E.A., Rosenbloom, K.R., Kent, W.J., Bouffard, G.G., Guan, X., Hansen, N.F., Idol, J.R., Maduro, V.V.B., Maskeri, B., McDowell, J.C., Park, M., Thomas, P.J., Young, A.C., Blakesley, R.W., Muzny, D.M., Sodergren, E., Wheeler, D.A., Worley, K.C., Jiang, H., Weinstock, G.M., Gibbs, R.A., Graves, T., Fulton, R., Mardis, E.R., Wilson, R.K., Clamp, M., Cuff, J., Gnerre, S., Jaffe, D.B., Chang, J.L., Lindblad-Toh, K., Lander, E.S., Hinrichs, A., Trumbower, H., Clawson, H., Zweig, A., Kuhn, R.M., Barber, G., Harte, R., Karolchik, D., Field, M.A., Moore, R.A., Matthewson, C.A., Schein, J.E., Marra, M.A., Antonarakis, S.E., Batzoglou, S., Goldman, N., Hardison, R., Haussler, D., Miller, W., Pachter, L., Green, E.D., Sidow, A. (2007)
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Gen. Res. 17, 760-774.
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Phylogenetic Methods
Massingham, T., Goldman, N. (2007)
Statistics of the log-det estimator.
Mol. Biol. Evol. 24, 2277-2285.
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Phylogenetic Diversity
Pardi, F., Goldman, N. (2007)
Resource aware taxon selection for maximizing phylogenetic diversity
Syst. Biol. 56, 431-444
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Databases
Taylor, M., Valdar, W., Kumar, A., Flint, J., Mott, R. (2007)
Management, presentation and interpretation of genome scans using GSCANDB
Bioinformatics 23, 1545-1549
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Models
Thorne, J.L., Goldman, N. (2007)
Probabilistic models for the study of protein evolution.
Balding, D.J., Bishop, M., Cannings, C. (Eds.), Handbook of Statistical Genetics. John Wiley, Chichester, UK, pp. 439-459.

Phylogenetic Methods
Whelan, S. (2007)
New approaches to phylogenetic tree search and their application to large numbers of protein alignments
Syst. Biol. 56, 727-740
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2006


Thesis
Bofkin, L. (2006)
The Causes and Consequences of Variation in Evolutionary Processes Acting on DNA Sequences
PhD thesis, University of Cambridge, Cambridge.
thesis PDF

Applications
David, L., Huber, W., Granovskaia, M., Toedling, J., Palm, C.J., Bofkin, L., Jones, T., Davis, R.W., Steinmetz, L.M. (2006)
A high-resolution map of transcription in the yeast genome
Proc. Natl. Acad. Sci. USA 103, 5320-5325.
citation detail

Models
Klosterman, P.S., Uzilov, A.V., Bendana, Y.R., Bradley, R.K., Chao, S., Kosiol, C., Goldman, N., Holmes, I. (2006)
XRate: a fast prototyping, training and annotation tool for phylo-grammars
BMC Bioinformatics 7, 428
citation detail

Thesis
Kosiol, C. (2006)
Markov Models for Protein Sequence Evolution
PhD thesis, University of Cambridge, Cambridge.
thesis PDF

Miscellaneous
Kosiol, C., Bofkin, L., Whelan, S. (2006)
Phylogenetics by likelihood: evolutionary modeling as a tool for understanding the genome
Journal of Biomedical Informatics 39, 51-61
citation detail

Databases
Whelan, S., de Bakker, P.I.W., Quevillon, E., Rodriguez, N., Goldman, N. (2006)
PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees
Nucl. Acids Res. 34, D327-D331.
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2005


Models
Kosiol, C., and Goldman, N. (2005)
Different versions of the Dayhoff rate matrix.
Mol. Biol. Evol. 22, 193-199
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Alignment
Löytynoja, A. and Goldman, N. (2005)
An algorithm for progressive multiple alignment of sequences with insertions.
Proc. Natl. Acad. Sci. USA 102, 10557-10562
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Phylogenetic Methods
Massingham, T., and Goldman, N. (2005)
Detecting amino acid sites under positive and purifying selection.
Genetics 169, 1753-1762
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Structure, evolution and HMMS
Meyer, I.M., Miklós, I. (2005)
Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs
Nucl. Acids Res. 33, 6338-6348
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Miscellaneous
Miklós, I., Meyer, I.M. (2005)
A linear memory algorithm for Baum-Welch training.
BMC Bioinformatics 6, 231
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Miscellaneous
Miklós, I., Meyer, I.M., Nagy, B. (2005)
Moments of the Boltzmann distribution for RNA secondary structures
Bull. Math. Biol. 67, 1031-1047
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Phylogenetic Diversity
Pardi, F., Goldman, N. (2005)
Species choice for comparative genomics: being greedy works
PLoS Genetics 1, e71
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2004


Thesis
Bofkin, L., and Whelan, S. (2004)
Functional needles in a genomic haystack
Heredity 92, 363-364.
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Models
Kosiol, C., Goldman, N. and Buttimore, N. (2004)
A new criterion and method for amino acid classification
J. Theor. Biol. 228, 97-106
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Applications
Liò, P., and Goldman, N. (2004)
Phylogenomics and bioinformatics of SARS-CoV
Trends in Microbiology 12, 106-111
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Phylogenetic Methods
Whelan, S., and Goldman, N. (2004)
Estimating the frequency of events that cause multiple nucleotide changes
Genetics 167, 2027-2043
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Phylogenetic Methods
Wong, W.S.W., Yang, Z., Goldman, N. and Nielsen, R. (2004)
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
Genetics 168, 1041-1051
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2003


Applications
Hardison, R.C., Roskin, K.M., Yang, S., Diekhans, M., Kent, W.J., Weber, R., Elnitski, L., Li, J., O'Connor, M., Kolbe, M., Schwartz, S., Furey, T.S., Whelan, S., Goldman, N., Smit, A., Miller, W., Chiaromonte, F. and D. Haussler. (2003)
Co-variation in frequencies of substitution, deletion, transposition and recombination during eutherian evolution
Gen. Res. 13, 13-26.
citation detail

Miscellaneous
Liò, P. (2003)
Dimensionality and dependence problems in statistical genomics
Briefings in Bioinformatics 4, 168-177
citation detail

Miscellaneous
Liò, P. (2003)
Statistical bioinformatic methods in microbial genome analysis
BioEssays 25, 266-273
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Miscellaneous
Liò, P. (2003)
Wavelets in bioinformatics and computational biology: state of art and perspectives.
Bioinformatics 19, 2-9
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Applications
Liò, P., and Vannucci, M. (2003)
Investigating the evolution and structure of chemokine receptors
Gene 317, 29-37
citation detail

Structure, evolution and HMMS
Robinson, D.M., Jones, D.T., Kishino, H., Goldman, N. and J.L. Thorne. (2003)
Protein evolution with dependence among codons due to tertiary structure
Mol. Biol. Evol. 20, 1692-1704.
citation detail

Models
Thorne, J.L., and Goldman, N. (2003)
Probabilistic models for the study of protein evolution
Balding, D.J., Bishop, M., Cannings, C. (Eds.), Handbook of Statistical Genetics. John Wiley, Chichester, UK, pp. 209-226

Databases
Whelan, S., de Bakker, P.I.W. and Goldman, N. (2003)
Pandit: a database of protein and associated nucleotide domains with inferred trees
Bioinformatics 19, 1556-1563
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2002


Applications
Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., ..., Goldman, N., ..., Whelan, S., ... and Lander, E.S. (2002)
Initial sequencing and comparative analysis of the mouse genome
Nature 420, 520-562
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Phylogenetic Methods
Goldman, N. and Whelan, S. (2002)
A novel use of equilibrium frequencies in models of sequence evolution.
Mol. Biol. Evol. 19, 1821-1831
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Structure, evolution and HMMS
Liò, P. and Goldman, N. (2002)
Modeling mitochondrial protein evolution using structural information
J. Mol. Evol. 54, 519-529
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2001


Models
Thorne, J.L. and Goldman, N. (2001)
Probabilistic models for the study of protein evolution
Balding, D.J., Bishop, M., Cannings, C. (Eds.), Handbook of Statistical Genetics. John Wiley, Chichester, UK, pp. 67-82

Models
Whelan, S. and Goldman, N. (2001)
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
Mol. Biol. Evol. 18, 691-699
citation detail

Phylogenetic Methods
Whelan, S., Liò, P. and Goldman, N. (2001)
Molecular phylogenetics: state of the art methods for looking into the past
Trends Gen. 17, 262-272
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2000


Phylogenetic Methods
Goldman, N., Anderson, J.P. and Rodrigo, A.G. (2000)
Likelihood-based tests of topologies in phylogenetics
Syst. Biol. 49, 652-670
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Phylogenetic Methods
Goldman, N. and Whelan, S. (2000)
Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics
Mol. Biol. Evol. 17, 975-978
citation detail

Applications
Hagelberg, E., Goldman, N., Liò, P., Whelan, S., Schiefenhövel, W., Clegg, J.B., Bowden, D.K. (2000)
Evidence for mitochondrial DNA recombination in a human population of island Melanesia: correction
Proc. R. Soc. Lond. B 267, 1595-1596.
citation detail

Phylogenetic Information
Massingham, T. and Goldman, N. (2000)
EDIBLE: experimental design and information calculations in phylogenetics
Bioinformatics 16, 294-295
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Models
Yang, Z., Nielsen, R., Goldman, N. and Pedersen, A.-M.K. (2000)
Codon-substitution models for heterogeneous selection pressure at amino acid sites
Genetics 155, 431-449
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1988-1999


Applications
Hagelberg, E., Goldman, N., Liò, P., Whelan, S., Schiefenhövel, W., Clegg, J.B., Bowden, D. (1999)
Evidence for mitochondrial DNA recombination in a human population of island Melanesia.
Proceedings of the Royal Society of London B 266:485-492.
Proc. R. Soc. Lond. B 266, 485-492
citation detail

Structure, evolution and HMMS
Liò, P. and Goldman, N. (1999)
Using protein structural information in evolutionary inference: transmembrane proteins.
Mol. Biol. Evol. 16, 1696-1710.
citation detail

Structure, evolution and HMMS
Pollock, D.D., Taylor, W.R. and Goldman, N. (1999)
Coevolving protein residues: maximum likelihood identification and relationship to structure
J. Mol. Biol. 287, 187-198
citation detail

Phylogenetic Methods
Whelan, S. and Goldman, N. (1999)
Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics
Mol. Biol. Evol. 16, 1292-1299.

Structure, evolution and HMMS
Goldman, N., Thorne, J.L. and Jones, D.T. (1998)
Assessing the impact of secondary structure and solvent accessibility on protein evolution
Genetics 149, 445-458
citation detail

Alignment
Goldman, N. (1998)
Effects of sequence alignment procedures on estimates of phylogeny
BioEssays 20, 287-290

Phylogenetic Information
Goldman, N. (1998)
Phylogenetic information and experimental design in molecular systematics
Proc. R. Soc. Lond. B 265, 1779-1786
citation detail

Models
Liò, P. and Goldman, N. (1998)
Models of molecular evolution and phylogeny
Gen. Res. 8, 1233-1244
citation detail

Structure, evolution and HMMS
Liò, P., Goldman, N., Thorne, J.L. and Jones, D.T. (1998)
PASSML: combining evolutionary inference and protein secondary structure prediction
Bioinformatics 14, 726-733
citation detail

Structure, evolution and HMMS
Goldman, N., Thorne, J.L., Jones, D.T. (1997)
Hidden Markov models for inferring evolutionary trees and predicting protein secondary structure. Proceedings of the 51st Session, Book 2 (Bulletin of the International Statistical Institute).
State Institute of Statistics, Istanbul, Turkey, pp. 233-236.

Phylogenetic Methods
Strimmer, K., Goldman, N. and von Haeseler, A. (1997)
Bayesian probabilities and quartet puzzling
Mol. Biol. Evol. 14, 210-211

Phylogenetic Methods
Yang, Z. and Goldman, N. (1997)
Are big trees indeed easy?
TREE 12, 357

Phylogenetic Methods
Goldman, N. (1996)
Phylogenetic estimation
Bishop, M.J., Rawlings, C.J. (Eds.), DNA and protein sequence analysis. IRL Press, Oxford, pp. 279-312

Structure, evolution and HMMS
Goldman, N., Thorne, J.L. and Jones, D.T. (1996)
Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses
J. Mol. Biol. 263, 196-208
citation detail

Structure, evolution and HMMS
Thorne, J.L., Goldman, N. and Jones, D.T. (1996)
Combining protein evolution and secondary structure.
Mol. Biol. Evol. 13, 666-673.
citation detail

Applications
Breuer, J., Douglas, N.W., Goldman, N. and Daniels, RS. (1995)
Human immunodeficiency virus type 2 (HIV-2) {Ienv} gene analysis: prediction of glycoprotein epitopes important for heterotypic neutralization and evidence for three genotype clusters within the HIV-2a subtype
J. Gen. Virol. 76, 333-345
citation detail

Models
Goldman, N. (1995)
Estimation of parameters of evolutionary models, with applications in the analysis of large data sets. In: Tavaré, S. (Ed.), Proceedings of Phylogeny Workshop,
DIMACS Technical Report 95-48. DIMACS, Princeton University, NJ, pp. 26-27

Phylogenetic Methods
Yang, Z., Goldman, N. and Friday, A. (1995)
Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem.
Syst. Biol. 44, 384-399
citation detail

Structure, evolution and HMMS
Thorne, J.L., Goldman, N., Jones, D.T. (1995)
Combining protein secondary structure and evolution
Tavaré, S. (Ed.), Proceedings of Phylogeny Workshop, DIMACS Technical Report 95-48. DIMACS, Princeton University, NJ, pp. 62-64
citation detail

Phylogenetic Methods
Gardner, M.J., Goldman, N., Barnett, P., Moore, P.W., Rangachari, K., Strath, M., Whyte, A., Williamson, D.H., Wilson, R.J.M. (1994)
Phylogenetic analysis of the rpoB gene from the plastid-like DNA of Plasmodium falciparum.
Mol. Biochem. Parasitol. 66, 221-231
citation detail

Phylogenetic Methods
Goldman, N. (1994)
Variance to mean ratio, R(t), for Poisson processes on phylogenetic trees.
Mol. Phyl. Evol. 3, 230-239
citation detail

Models
Goldman, N. and Yang, Z. (1994)
A codon-based model of nucleotide substitution for protein-coding DNA sequences
Mol. Biol. Evol. 11, 725-736
citation detail

Models
Goldman, N. and Yang, Z. (1994)
Models of DNA substitution and the discrimination of evolutionary parameters. Proceedings of the XVIIth International Biometrics Conference, Hamilton, Ontario, Canada
International Biometric Society, Hamilton, Ontario, Canada, pp. 407-421

Phylogenetic Methods
Yang, Z., Goldman, N. (1994)
Evaluation and extension of Markov process models for the evolution of DNA
(in Chinese, with Abstract in English). Acta Genetica Sinica 21, 17-23
citation detail

Phylogenetic Methods
Yang, Z., Goldman, N. and Friday, A. (1994)
Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation
Mol. Biol. Evol. 11, 316-324
citation detail

Miscellaneous
Goldman, N. (1993)
Further results on error minimization in the genetic code
J. Mol. Evol. 37, 662-664
citation detail

Miscellaneous
Goldman, N. (1993)
Nucleotide, dinucleotide and trinucleotide frequencies explain patterns observed in chaos game representations of DNA sequences
Nucl. Acids Res. 21, 2487-2491.
citation detail

Phylogenetic Methods
Goldman, N. (1993)
Simple diagnostic statistical tests of models for DNA substitution
J. Mol. Evol. 37, 650-661
citation detail

Phylogenetic Methods
Goldman, N. (1993)
Statistical tests of models of DNA substitution
J. Mol. Evol. 36, 182-198
citation detail

Thesis
Goldman, N. (1992)
Statistical Estimation of Evolutionary Trees
University of Cambridge, Cambridge

Miscellaneous
Goldman, N. and Barton, N. (1992)
Human origins: genetics and geography
Nature 357, 440-441
citation detail

Phylogenetic Methods
Goldman, N. (1990)
Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analyses.
Syst. Zool. 39, 345-361

Miscellaneous
Goldman, N., Paddock, T.B.B., Shaw, K.M. (1990)
Quantitative analysis of shape variation in populations of Surirella fastuosa
Diatom Res. 5, 25-42.

Phylogenetic Methods
Goldman, N. (1989)
Fewest variables coding method for multistate characters
Syst. Zool. 38, 79-85

Miscellaneous
Goldman, N., Lambshead, P.J.D. (1989)
Optimization of the Ewens/Caswell neutral model program for community diversity analysis
Mar. Ecol. Prog. Ser. 50, 255-261

Phylogenetic Methods
Goldman, N. (1988)
Methods for discrete coding of morphological characters for numerical analysis
Cladistics 4, 59-71

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