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Cleaned up citations
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dhuson committed Mar 14, 2024
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Expand Up @@ -45,7 +45,7 @@ public class Codominant extends Characters2Distances {

@Override
public String getCitation() {
return "Smouse & Peakall 1999; Smouse PE, Peakall R. Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity, 82, 561-573, 1999.";
return "Smouse & Peakall 1999; PE Smouse and R. Peakall. Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity, 82:561573, 1999.";
}

@Override
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Expand Up @@ -40,7 +40,7 @@
public class Dice extends Characters2Distances {
@Override
public String getCitation() { // is this the correct citation?
return "Dice 1945; Dice, Lee R. (1945). Measures of the Amount of Ecologic Association Between Species. Ecology. 26 (3): 297–302.";
return "Dice 1945;LR Dice. Measures of the amount of ecologic association between species. Ecology, 26(3):297–302, 1945.";
}

@Override
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Expand Up @@ -43,9 +43,7 @@ public enum Method {MLE, SharedGenes}

@Override
public String getCitation() {
return (getOptionMethod() == Method.MLE ?
"Huson & Steel 2004; D.H. Huson and M. Steel. Phylogenetic trees based on gene content. Bioinformatics, 20(13):2044–9, 2004." :
"Snel et al 1997; B. Snel, P. Bork and MA Huynen. Genome phylogeny based on gene content, Nature Genetics, 21:108-110, 1997.");
return "Huson & Steel 2004; DH Huson and MA Steel. Phylogenetic trees based on gene content. Bioinformatics, 20(13):2044–2049, 2004.";
}

@Override
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Expand Up @@ -49,7 +49,7 @@ public List<String> listOptions() {

@Override
public String getCitation() {
return "Hamming 1950; Hamming, Richard W. Error detecting and error correcting codes. Bell System Technical Journal. 29 (2): 147–160. MR 0035935, 1950.";
return "Hamming 1950;RW Hamming. Error detecting and error correcting codes. Bell System Technical Journal, 29(2):147–160 1950.";
}

@Override
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Expand Up @@ -37,7 +37,7 @@
public class Jaccard extends Characters2Distances {
@Override
public String getCitation() {
return "Jaccard 1901; Jaccard, Paul (1901). Étude comparative de la distribution florale dans une portion des Alpes et des Jura, Bulletin de la Société Vaudoise des Sciences Naturelles, 37: 547–579.";
return "Jaccard 1901; P. Jaccard. Étude comparative de la distribution florale dans une portion des Alpes et des Jura, Bulletin de la Société Vaudoise des Sciences Naturelles, 37: 547–579, 1901.";
}

@Override
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Expand Up @@ -94,7 +94,7 @@ public class LogDet extends Characters2Distances {

@Override
public String getCitation() {
return "Steel 1994; M.A. Steel. Recovering a tree from the leaf colorations it generates under a Markov model. Appl. Math. Lett., 7(2):19–24, 1994.";
return "Steel 1994; MA Steel. Recovering a tree from the leaf colorations it generates under a Markov model. Appl. Math. Lett., 7(2):19–24, 1994.";
}

@Override
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Expand Up @@ -43,7 +43,7 @@ public class NeiLiRestrictionDistance extends Characters2Distances {

@Override
public String getCitation() {
return "Nei & Li 1979;M Nei and W H Li. Mathematical model for studying genetic variation in terms of restriction endonucleases, PNAS 79(1):5269-5273, 1979.";
return "Nei & Li 1979;M Nei and WH Li. Mathematical model for studying genetic variation in terms of restriction endonucleases, PNAS 79(1):5269-5273, 1979.";
}

@Override
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Expand Up @@ -35,8 +35,7 @@
public class NeiMiller extends Characters2Distances {
@Override
public String getCitation() {
return "Nei & Miller 1990; M. Nei and J.C. Miller. " +
"A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. " +
return "Nei & Miller 1990; M. Nei and JC Miller. A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. " +
"Genetics, 125:873–879, 1990.";
}

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Expand Up @@ -50,8 +50,8 @@ public String getToolTip(String optionName) {

@Override
public String getCitation() {
return "Upholt 1977; Upholt WB. Estimation of DNA sequence divergence from comparison of restriction endonuclease digests. " +
"Nucleic Acids Res. 1977;4(5):1257-65.";
return "Upholt 1977; WB Upholt. Estimation of DNA sequence divergence from comparison of restriction endonuclease digests. " +
"Nucleic Acids Res., 4(5):1257-65, 1997.";
}

@Override
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Expand Up @@ -37,12 +37,12 @@
public class F81 extends Nucleotides2DistancesBase {
@Override
public String getCitation() {
return "Felsenstein 1981; Felsenstein J (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution. 17 (6): 368–376.";
return "Felsenstein 1981; J. Felsenstein, Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution. 17 (6): 368–376, 1981.";
}

@Override
public String getShortDescription() {
return "Calculates distances under the Felsenstein81 model.";
return "Calculates distances under the Felsenstein-81 model.";
}

@Override
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Expand Up @@ -37,12 +37,12 @@
public class F84 extends Nucleotides2DistancesBase {
@Override
public String getCitation() {
return "Felsenstein & Churchill 1996; Felsenstein J, Churchill GA (1996). A Hidden Markov Model approach to variation among sites in rate of evolution, and the branching order in hominoidea. Molecular Biology and Evolution. 13 (1): 93–104.";
return "Felsenstein & Churchill 1996; J. Felsenstein and GA Churchill. A Hidden Markov Model approach to variation among sites in rate of evolution, and the branching order in hominoidea. Molecular Biology and Evolution. 13 (1): 93–104, 1996.";
}

@Override
public String getShortDescription() {
return "Calculates distances under the Felsenstein84 model.";
return "Calculates distances under the Felsenstein-84 model.";
}

@Override
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Expand Up @@ -38,7 +38,7 @@
public class GTR extends Nucleotides2DistancesBase {
@Override
public String getCitation() {
return "Tavaré 1986; Tavaré S (1986). Some Probabilistic and Statistical Problems in the Analysis of DNA Sequences. Lectures on Mathematics in the Life Sciences. 17: 57–86";
return "Tavaré 1986; S. Tavaré. Some Probabilistic and Statistical Problems in the Analysis of DNA Sequences. Lectures on Mathematics in the Life Sciences. 17:57–86, 1986.";
}

@Override
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Expand Up @@ -41,8 +41,8 @@ public class HKY85 extends Nucleotides2DistancesBase {
@Override
public String getCitation() {
return "Hasegawa et al 1985;" +
" Hasegawa M, Kishino H, Yano T. Dating of human-ape splitting by a molecular clock of mitochondrial DNA." +
" Journal of Molecular Evolution. 22 (2): 160–174. PMID 3934395. doi:10.1007/BF02101694, 1985.";
" M. Hasegawa, H. Kishino and T. Yano. Dating of human-ape splitting by a molecular clock of mitochondrial DNA." +
" Journal of Molecular Evolution. 22(2):160–174, 1985.";
}

@Override
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Expand Up @@ -35,7 +35,7 @@
public class JukesCantor extends Nucleotides2DistancesBase {
@Override
public String getCitation() {
return "Jukes & Cantor 1969; Jukes TH & Cantor CR (1969). Evolution of Protein Molecules. New York: Academic Press. pp. 21–132";
return "Jukes & Cantor 1969; TH Jukes Tand CR Cantor CR. Evolution of Protein Molecules. New York: Academic Press., 21–132, 1996.";
}

@Override
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Expand Up @@ -40,7 +40,7 @@
public class K2P extends Nucleotides2DistancesBase {
@Override
public String getCitation() {
return "Kimura 1980; Kimura M (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution. 16 (2): 111–120.";
return "Kimura 1980; M. Kimura. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution. 16(2):111–120, 1980.";
}

@Override
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Expand Up @@ -45,8 +45,7 @@ public class K3ST extends Nucleotides2DistancesBase {

@Override
public String getCitation() {
return "Kimura 1981; M. Kimura, Estimation of evolutionary sequences between homologous nucleotide sequences, " +
"Proc. Natl. Acad. Sci. USA 78 (1981) 454–45";
return "Kimura 1981; M. Kimura, Estimation of evolutionary sequences between homologous nucleotide sequences, PNAS, 78:454–45, 1981.";
}

@Override
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Expand Up @@ -79,7 +79,7 @@ public boolean isApplicable(TaxaBlock taxa, CharactersBlock chars) {

@Override
public String getCitation() {
return "Bandelt et al 1999;H. -J. Bandelt, P. Forster, and A. Röhl. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16:37–48, 1999.";
return "Bandelt et al 1999;HJ Bandelt, P. Forster, and A. Röhl. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16:37–48, 1999.";
}

public int getOptionEpsilon() {
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Expand Up @@ -46,7 +46,7 @@ public class EstimateInvariableSites extends AnalyzeCharactersBase {

@Override
public String getCitation() {
return "Steel et al 2000;MA Steel, DH Huson, and PJ Lockhart. Invariable site models and their use in phylogeny reconstruction. Sys. Biol. 49(2):225-232, 2000";
return "Steel et al 2000;MA Steel, DH Huson, and PJ Lockhart. Invariable site models and their use in phylogeny reconstruction. Sys. Biol. 49(2):225-232, 2000.";
}

@Override
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Expand Up @@ -51,8 +51,7 @@ public class PhiTest extends AnalyzeCharactersBase {

@Override
public String getCitation() {
return "Bruen et al 2006; " +
"Bruen TC, Philippe H, Bryant D. A simple and robust statistical test for detecting the presence of recombination. Genetics 17(4):2665-81, 2006";
return "Bruen et al 2006;TC Bruen, H. Philippe and D. Bryant. A simple and robust statistical test for detecting the presence of recombination. Genetics 17(4):2665-81, 2006.";
}

@Override
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Expand Up @@ -68,7 +68,7 @@ public String getToolTip(String optionName) {

@Override
public String getCitation() {
return "Huson et al 2012;D.H. Huson, R. Rupp and C. Scornavacca, Phylogenetic Networks, Cambridge, 2012.";
return "Huson et al 2012;DH Huson, R. Rupp and C. Scornavacca, Phylogenetic Networks, Cambridge, 2012.";
}

@Override
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Expand Up @@ -171,7 +171,7 @@ else if ("ctuybh".indexOf(ch) >= 0)

@Override
public String getCitation() {
return "Huson et al 2012;D.H. Huson, R. Rupp and C. Scornavacca, Phylogenetic Networks, Cambridge, 2012.";
return "Huson et al 2012;DH Huson, R. Rupp and C. Scornavacca, Phylogenetic Networks, Cambridge, 2012.";
}

@Override
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Expand Up @@ -43,7 +43,7 @@ public class ParsimonySplits extends Characters2Splits {

@Override
public String getCitation() {
return "Bandelt and Dress 1992; H.-J.Bandelt and A.W.M.Dress. A canonical decomposition theory for metrics on a finite set. Advances in Mathematics, 92:47–105, 1992.";
return "Bandelt & Dress 1992; HJ Bandelt and AWM Dress. A canonical decomposition theory for metrics on a finite set. Advances in Mathematics, 92:47–105, 1992.";
}

@Override
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Expand Up @@ -43,7 +43,7 @@
public class MinSpanningNetwork extends Distances2Network {
@Override
public String getCitation() {
return "Excoffier & Smouse 1994; Excoffier L, Smouse PE. Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony (1994) Genetics.136(1):343-59.";
return "Excoffier & Smouse 1994; L. Excoffier and PE Smouse. Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony, Genetics.136(1):343-59, 1994.";
}

@Override
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Expand Up @@ -55,7 +55,7 @@ public class PCoA extends Distances2Network {

@Override
public String getCitation() {
return "Gower 1966; Gower, J. C. (1966). Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika, 53(3-4), 325-338.";
return "Gower 1966; JC Gower,. Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika, 53(3-4):325-338, 1996.";
}

@Override
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Expand Up @@ -36,7 +36,7 @@ public class DeltaScore extends Distances2ReportBase {
@Override
public String getCitation() {
return "Holland et al 2002;" +
"B. R. Holland, K. T. Huber, A. Dress, V. Moulton, Delta Plots: A tool for analyzing phylogenetic distance data, Molecular Biology and Evolution, 19(12):2051–2059, 2002.";
"BR Holland, KT Huber, AWM Dress and V. Moulton, Delta Plots: A tool for analyzing phylogenetic distance data, Molecular Biology and Evolution, 19(12):2051–2059, 2002.";
}

@Override
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Expand Up @@ -43,7 +43,7 @@
public class BunemanTree extends Distances2Splits implements IToCompatibleSplits {
@Override
public String getCitation() {
return "Bandelt & Dress 1992; H.-J. Bandelt and A.W.M.Dress. A canonical decomposition theory for metrics on a finite set. " +
return "Bandelt & Dress 1992; HJ Bandelt and AWM Dress. A canonical decomposition theory for metrics on a finite set. " +
"Advances in Mathematics, 92:47–105, 1992.";
}

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Expand Up @@ -68,7 +68,7 @@ public String getCitation() {
return "Bryant & Moulton 2004; " +
"D. Bryant and V. Moulton. Neighbor-net: An agglomerative method for the construction of phylogenetic networks. " +
"Molecular Biology and Evolution, 21(2):255– 265, 2004.;" +
"Bryant & Huson 2023;D. Bryant and D.H. Huson, NeighborNet- improved algorithms and implementation. Front. Bioinform. 3, 2023";
"Bryant & Huson 2023;D. Bryant and DH Huson, NeighborNet- improved algorithms and implementation. Front. Bioinform. 3, 2023.";
}

@Override
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Expand Up @@ -41,7 +41,7 @@ public class SplitDecomposition extends Distances2Splits {

@Override
public String getCitation() {
return "Bandelt & Dress 1992; H.-J.Bandelt and A.W.M.Dress. A canonical decomposition theory for metrics on a finite set. Advances in Mathematics, 92:47–105, 1992.";
return "Bandelt & Dress 1992; HJ Bandelt and AWM Dress. A canonical decomposition theory for metrics on a finite set. Advances in Mathematics, 92:47–105, 1992.";
}

@Override
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Expand Up @@ -47,7 +47,7 @@ public class BioNJ extends Distances2Trees implements IToSingleTree {
public String getCitation() {
return "Gascuel 1997; " +
"O. Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. " +
"Molecular Biology and Evolution. 1997 14:685-695.";
"Molecular Biology and Evolution. 14:685-695, 1997.";
}

@Override
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Expand Up @@ -63,7 +63,7 @@ public List<String> listOptions() {

@Override
public String getCitation() {
return "Ondov et al 2016; Brian D. Ondov, Todd J. Treangen, Páll Melsted, Adam B. Mallonee, Nicholas H. Bergman, Sergey Koren & Adam M. Phillippy. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 17, 132 (2016).";
return "Ondov et al 2016; BD Ondov, TJ Treangen, P. Melsted, AB Mallonee, NH Bergman, S. Koren & AM Phillippy. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 17:132, 2016.";
}

@Override
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Expand Up @@ -44,8 +44,8 @@ String runAnalysis(ProgressListener progress, TaxaBlock taxaBlock, SplitsBlock s

@Override
public String getCitation() {
return "Volkmann et al 2014;Volkmann L, Martyn I, Moulton V, Spillner A, Mooers AO." +
" Prioritizing populations for conservation using phylogenetic networks. PLoS ONE 9(2):e88945 (2014)";
return "Volkmann et al 2014;L. Volkmann, I. Martyn, V. Moulton, A. Spillner, and AO Mooers." +
" Prioritizing populations for conservation using phylogenetic networks. PLoS ONE 9(2):e88945, 2014.";
}

@Override
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Expand Up @@ -43,8 +43,8 @@ String runAnalysis(ProgressListener progress, TaxaBlock taxaBlock, SplitsBlock s

@Override
public String getCitation() {
return "Volkmann et al 2014;Volkmann L, Martyn I, Moulton V, Spillner A, Mooers AO." +
" Prioritizing populations for conservation using phylogenetic networks. PLoS ONE 9(2):e88945 (2014)";
return "Volkmann et al 2014;L. Volkmann, I. Martyn, V. Moulton, A. Spillner, and AO Mooers." +
" Prioritizing populations for conservation using phylogenetic networks. PLoS ONE 9(2):e88945, 2014";
}

@Override
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Expand Up @@ -302,6 +302,6 @@ public static DataBlock run(ProgressListener progress, TaxaBlock taxa, Character

@Override
public String getCitation() {
return "Felsenstein 1985;Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39(4):783-791";
return "Felsenstein 1985;J. Felsenstein. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39(4):783-791, 1985.";
}
}
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Expand Up @@ -37,7 +37,7 @@
public class GreedyTree extends Splits2Trees {
@Override
public String getCitation() {
return "Huson et al 2012;D.H. Huson, R. Rupp and C. Scornavacca, Phylogenetic Networks, Cambridge, 2012.";
return "Huson et al 2012;DH Huson, R. Rupp and C. Scornavacca, Phylogenetic Networks, Cambridge, 2012.";
}

public String getShortDescription() {
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Expand Up @@ -45,7 +45,7 @@ public class AverageDistances extends Trees2Distances {
public String getCitation() {
return "Lapointe and Cucumel 1997;FJ Lapointe and G. Cucumel, " +
"The Average Consensus Procedure: Combination of Weighted Trees Containing Identical or Overlapping Sets of Taxa. " +
"Systematic Biology, 46(2):306-312 (1997).";
"Systematic Biology, 46(2):306-312, 1997.";
}

@Override
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Expand Up @@ -64,7 +64,7 @@ public String getToolTip(String optionName) {

@Override
public String getCitation() {
return "Faith 1992;Faith, D.P. Conservation evaluation and phylogenetic diversity. Biological Conservation 61, 1–10 (1992)";
return "Faith 1992;DP Faith. Conservation evaluation and phylogenetic diversity. Biological Conservation 61, 1–10, 1992.";
}

@Override
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Expand Up @@ -64,8 +64,8 @@ public String getToolTip(String optionName) {

@Override
public String getCitation() {
return "Redding 2003;D. Redding, Incorporating genetic distinctness and reserve occupancy into a conservation priorisation approach. Master’s thesis. University of East Anglia (2003);" +
"Redding & Mooers 2006;Redding, D.W., Mooers, A.Ø. Incorporating evolutionary measures into conservation prioritization. Conservation Biology 20, 1670–1678 (2006)";
return "Redding 2003;D. Redding, Incorporating genetic distinctness and reserve occupancy into a conservation priorisation approach. Master’s thesis. University of East Anglia, 2003.;" +
"Redding & Mooers 2006;DW Redding and AO Mooers. Incorporating evolutionary measures into conservation prioritization. Conservation Biology 20, 1670–1678, 2006.";
}

@Override
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Expand Up @@ -46,7 +46,7 @@ String runAnalysis(ProgressListener progress, TaxaBlock taxaBlock, TreesBlock tr

@Override
public String getCitation() {
return "Haake et al 2008;Haake C.J., Kashiwada A., Su F.E. The Shapley value of phylogenetic trees. J Math Biol 56:479–497 (2008) ";
return "Haake et al 2008;CJ Haake, A. Kashiwada and FE Su. The Shapley value of phylogenetic trees. J Math Biol 56:479–497, 2008.";
}

@Override
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Expand Up @@ -69,7 +69,7 @@ public enum Reference {MajorityConsensus, FirstInputTree, LastInputTree}

@Override
public String getCitation() {
return "Huson et al. 2020;D.H. Huson, M.A. Steel and others. Anti-consensus: manuscript in preparation";
return "Huson et al. 2020;DH Huson, MA Steel and others. Anti-consensus: manuscript in preparation.";
}

@Override
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Expand Up @@ -37,9 +37,9 @@
public class AverageConsensus extends Trees2Splits {
@Override
public String getCitation() {
return "Lapointe and Cucumel 1997;FJ Lapointe and G. Cucumel, " +
return "Lapointe and Cucumel 1997;FJ Lapointe and G. Cucumel. " +
"The Average Consensus Procedure: Combination of Weighted Trees Containing Identical or Overlapping Sets of Taxa. " +
"Systematic Biology, 46(2):306-312 (1997).";
"Systematic Biology, 46(2):306-312, 1997.";
}

public String getShortDescription() {
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