From 009aa9caba21a6197e72d6a2d96e39ebe28ff977 Mon Sep 17 00:00:00 2001 From: Daniel Date: Thu, 14 Mar 2024 15:35:47 +1300 Subject: [PATCH] Cleaned up citations --- .../characters/characters2distances/Codominant.java | 2 +- .../algorithms/characters/characters2distances/Dice.java | 2 +- .../characters/characters2distances/GeneContentDistance.java | 4 +--- .../characters/characters2distances/HammingDistances.java | 2 +- .../algorithms/characters/characters2distances/Jaccard.java | 2 +- .../algorithms/characters/characters2distances/LogDet.java | 2 +- .../characters2distances/NeiLiRestrictionDistance.java | 2 +- .../algorithms/characters/characters2distances/NeiMiller.java | 3 +-- .../algorithms/characters/characters2distances/Upholt.java | 4 ++-- .../characters/characters2distances/nucleotide/F81.java | 4 ++-- .../characters/characters2distances/nucleotide/F84.java | 4 ++-- .../characters/characters2distances/nucleotide/GTR.java | 2 +- .../characters/characters2distances/nucleotide/HKY85.java | 4 ++-- .../characters2distances/nucleotide/JukesCantor.java | 2 +- .../characters/characters2distances/nucleotide/K2P.java | 2 +- .../characters/characters2distances/nucleotide/K3ST.java | 3 +-- .../characters/characters2network/MedianJoining.java | 2 +- .../characters/characters2report/EstimateInvariableSites.java | 2 +- .../algorithms/characters/characters2report/PhiTest.java | 3 +-- .../characters/characters2splits/BinaryToSplits.java | 2 +- .../algorithms/characters/characters2splits/DnaToSplits.java | 2 +- .../characters/characters2splits/ParsimonySplits.java | 2 +- .../distances/distances2network/MinSpanningNetwork.java | 2 +- .../algorithms/distances/distances2network/PCoA.java | 2 +- .../algorithms/distances/distances2report/DeltaScore.java | 2 +- .../algorithms/distances/distances2splits/BunemanTree.java | 2 +- .../algorithms/distances/distances2splits/NeighborNet.java | 2 +- .../distances/distances2splits/SplitDecomposition.java | 2 +- .../algorithms/distances/distances2trees/BioNJ.java | 2 +- .../splitstree6/algorithms/genomes/genome2distances/Mash.java | 2 +- .../splits/splits2report/PhylogeneticDiversity.java | 4 ++-- .../algorithms/splits/splits2report/ShapleyValues.java | 4 ++-- .../algorithms/splits/splits2splits/BootstrapSplits.java | 2 +- .../algorithms/splits/splits2trees/GreedyTree.java | 2 +- .../algorithms/trees/trees2distances/AverageDistances.java | 2 +- .../algorithms/trees/trees2report/PhylogeneticDiversity.java | 2 +- .../algorithms/trees/trees2report/TreeDiversityIndex.java | 4 ++-- .../algorithms/trees/trees2report/UnrootedShapleyValues.java | 2 +- .../algorithms/trees/trees2splits/AntiConsensusNetwork.java | 2 +- .../algorithms/trees/trees2splits/AverageConsensus.java | 4 ++-- .../algorithms/trees/trees2splits/ConsensusNetwork.java | 2 +- .../algorithms/trees/trees2splits/ConsensusOutline.java | 2 +- .../algorithms/trees/trees2splits/ConsensusSplits.java | 2 +- .../algorithms/trees/trees2splits/CredibilityNetwork.java | 2 +- .../algorithms/trees/trees2splits/FilteredSuperNetwork.java | 4 ++-- .../algorithms/trees/trees2splits/SuperNetwork.java | 2 +- .../algorithms/trees/trees2trees/ALTSExternal.java | 2 +- .../splitstree6/algorithms/trees/trees2trees/ALTSNetwork.java | 2 +- .../algorithms/trees/trees2trees/AutumnAlgorithm.java | 4 ++-- .../algorithms/trees/trees2trees/BootstrapTree.java | 4 ++-- .../algorithms/trees/trees2trees/ClusterNetwork.java | 2 +- .../algorithms/trees/trees2trees/ConsensusTree.java | 2 +- .../splitstree6/algorithms/trees/trees2trees/Trees2Trees.java | 2 +- .../java/splitstree6/view/trees/densitree/DensiTreeView.java | 2 +- .../splitstree6/view/trees/tanglegram/TanglegramView.java | 2 +- 55 files changed, 66 insertions(+), 71 deletions(-) diff --git a/src/main/java/splitstree6/algorithms/characters/characters2distances/Codominant.java b/src/main/java/splitstree6/algorithms/characters/characters2distances/Codominant.java index 0d8a2af4..30410010 100755 --- a/src/main/java/splitstree6/algorithms/characters/characters2distances/Codominant.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2distances/Codominant.java @@ -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, 82:561–573, 1999."; } @Override diff --git a/src/main/java/splitstree6/algorithms/characters/characters2distances/Dice.java b/src/main/java/splitstree6/algorithms/characters/characters2distances/Dice.java index b0eea441..a3d7af4c 100755 --- a/src/main/java/splitstree6/algorithms/characters/characters2distances/Dice.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2distances/Dice.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2distances/GeneContentDistance.java b/src/main/java/splitstree6/algorithms/characters/characters2distances/GeneContentDistance.java index ffa15011..e94b6fdd 100755 --- a/src/main/java/splitstree6/algorithms/characters/characters2distances/GeneContentDistance.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2distances/GeneContentDistance.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2distances/HammingDistances.java b/src/main/java/splitstree6/algorithms/characters/characters2distances/HammingDistances.java index a915dee2..423a5c14 100755 --- a/src/main/java/splitstree6/algorithms/characters/characters2distances/HammingDistances.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2distances/HammingDistances.java @@ -49,7 +49,7 @@ public List 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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2distances/Jaccard.java b/src/main/java/splitstree6/algorithms/characters/characters2distances/Jaccard.java index b9d29fdc..184fc89a 100755 --- a/src/main/java/splitstree6/algorithms/characters/characters2distances/Jaccard.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2distances/Jaccard.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2distances/LogDet.java b/src/main/java/splitstree6/algorithms/characters/characters2distances/LogDet.java index 9f56472f..1cd2e542 100755 --- a/src/main/java/splitstree6/algorithms/characters/characters2distances/LogDet.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2distances/LogDet.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2distances/NeiLiRestrictionDistance.java b/src/main/java/splitstree6/algorithms/characters/characters2distances/NeiLiRestrictionDistance.java index 52ab4c38..899eec10 100755 --- a/src/main/java/splitstree6/algorithms/characters/characters2distances/NeiLiRestrictionDistance.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2distances/NeiLiRestrictionDistance.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2distances/NeiMiller.java b/src/main/java/splitstree6/algorithms/characters/characters2distances/NeiMiller.java index 0e7d8015..dd0932f3 100755 --- a/src/main/java/splitstree6/algorithms/characters/characters2distances/NeiMiller.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2distances/NeiMiller.java @@ -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."; } diff --git a/src/main/java/splitstree6/algorithms/characters/characters2distances/Upholt.java b/src/main/java/splitstree6/algorithms/characters/characters2distances/Upholt.java index cdf54c92..4dea0a5c 100755 --- a/src/main/java/splitstree6/algorithms/characters/characters2distances/Upholt.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2distances/Upholt.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/F81.java b/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/F81.java index 54fc0005..c8618e4f 100755 --- a/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/F81.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/F81.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/F84.java b/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/F84.java index 4fe78d62..ed837db0 100755 --- a/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/F84.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/F84.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/GTR.java b/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/GTR.java index 6c158c38..85334cbe 100755 --- a/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/GTR.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/GTR.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/HKY85.java b/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/HKY85.java index 570d0ce1..18bb6eaf 100755 --- a/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/HKY85.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/HKY85.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/JukesCantor.java b/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/JukesCantor.java index 09933e91..33a97a38 100644 --- a/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/JukesCantor.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/JukesCantor.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/K2P.java b/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/K2P.java index 6e594101..1caa0819 100755 --- a/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/K2P.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/K2P.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/K3ST.java b/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/K3ST.java index 2fa7bf54..e3e97d81 100755 --- a/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/K3ST.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2distances/nucleotide/K3ST.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2network/MedianJoining.java b/src/main/java/splitstree6/algorithms/characters/characters2network/MedianJoining.java index 5fa9dc9c..597346be 100644 --- a/src/main/java/splitstree6/algorithms/characters/characters2network/MedianJoining.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2network/MedianJoining.java @@ -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() { diff --git a/src/main/java/splitstree6/algorithms/characters/characters2report/EstimateInvariableSites.java b/src/main/java/splitstree6/algorithms/characters/characters2report/EstimateInvariableSites.java index 1d86f151..2d5d79fd 100644 --- a/src/main/java/splitstree6/algorithms/characters/characters2report/EstimateInvariableSites.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2report/EstimateInvariableSites.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2report/PhiTest.java b/src/main/java/splitstree6/algorithms/characters/characters2report/PhiTest.java index 3ba5f589..4bb85323 100644 --- a/src/main/java/splitstree6/algorithms/characters/characters2report/PhiTest.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2report/PhiTest.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2splits/BinaryToSplits.java b/src/main/java/splitstree6/algorithms/characters/characters2splits/BinaryToSplits.java index 6dd3061b..26ca8141 100644 --- a/src/main/java/splitstree6/algorithms/characters/characters2splits/BinaryToSplits.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2splits/BinaryToSplits.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2splits/DnaToSplits.java b/src/main/java/splitstree6/algorithms/characters/characters2splits/DnaToSplits.java index 2270d271..f4c05681 100644 --- a/src/main/java/splitstree6/algorithms/characters/characters2splits/DnaToSplits.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2splits/DnaToSplits.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/characters/characters2splits/ParsimonySplits.java b/src/main/java/splitstree6/algorithms/characters/characters2splits/ParsimonySplits.java index b7be60ae..7a916715 100644 --- a/src/main/java/splitstree6/algorithms/characters/characters2splits/ParsimonySplits.java +++ b/src/main/java/splitstree6/algorithms/characters/characters2splits/ParsimonySplits.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/distances/distances2network/MinSpanningNetwork.java b/src/main/java/splitstree6/algorithms/distances/distances2network/MinSpanningNetwork.java index 1cda69bc..6647d104 100644 --- a/src/main/java/splitstree6/algorithms/distances/distances2network/MinSpanningNetwork.java +++ b/src/main/java/splitstree6/algorithms/distances/distances2network/MinSpanningNetwork.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/distances/distances2network/PCoA.java b/src/main/java/splitstree6/algorithms/distances/distances2network/PCoA.java index 84218a42..45057ed9 100644 --- a/src/main/java/splitstree6/algorithms/distances/distances2network/PCoA.java +++ b/src/main/java/splitstree6/algorithms/distances/distances2network/PCoA.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/distances/distances2report/DeltaScore.java b/src/main/java/splitstree6/algorithms/distances/distances2report/DeltaScore.java index 2e09438b..74c24de9 100644 --- a/src/main/java/splitstree6/algorithms/distances/distances2report/DeltaScore.java +++ b/src/main/java/splitstree6/algorithms/distances/distances2report/DeltaScore.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/distances/distances2splits/BunemanTree.java b/src/main/java/splitstree6/algorithms/distances/distances2splits/BunemanTree.java index 0013134c..34853fcb 100755 --- a/src/main/java/splitstree6/algorithms/distances/distances2splits/BunemanTree.java +++ b/src/main/java/splitstree6/algorithms/distances/distances2splits/BunemanTree.java @@ -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."; } diff --git a/src/main/java/splitstree6/algorithms/distances/distances2splits/NeighborNet.java b/src/main/java/splitstree6/algorithms/distances/distances2splits/NeighborNet.java index 1efd1c70..1206853a 100644 --- a/src/main/java/splitstree6/algorithms/distances/distances2splits/NeighborNet.java +++ b/src/main/java/splitstree6/algorithms/distances/distances2splits/NeighborNet.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/distances/distances2splits/SplitDecomposition.java b/src/main/java/splitstree6/algorithms/distances/distances2splits/SplitDecomposition.java index 30fb08a1..61da8009 100755 --- a/src/main/java/splitstree6/algorithms/distances/distances2splits/SplitDecomposition.java +++ b/src/main/java/splitstree6/algorithms/distances/distances2splits/SplitDecomposition.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/distances/distances2trees/BioNJ.java b/src/main/java/splitstree6/algorithms/distances/distances2trees/BioNJ.java index 54a18baa..a8536a22 100755 --- a/src/main/java/splitstree6/algorithms/distances/distances2trees/BioNJ.java +++ b/src/main/java/splitstree6/algorithms/distances/distances2trees/BioNJ.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/genomes/genome2distances/Mash.java b/src/main/java/splitstree6/algorithms/genomes/genome2distances/Mash.java index 1daf0116..fcfd4c5a 100644 --- a/src/main/java/splitstree6/algorithms/genomes/genome2distances/Mash.java +++ b/src/main/java/splitstree6/algorithms/genomes/genome2distances/Mash.java @@ -63,7 +63,7 @@ public List 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 diff --git a/src/main/java/splitstree6/algorithms/splits/splits2report/PhylogeneticDiversity.java b/src/main/java/splitstree6/algorithms/splits/splits2report/PhylogeneticDiversity.java index 08918a40..c37fa6d3 100644 --- a/src/main/java/splitstree6/algorithms/splits/splits2report/PhylogeneticDiversity.java +++ b/src/main/java/splitstree6/algorithms/splits/splits2report/PhylogeneticDiversity.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/splits/splits2report/ShapleyValues.java b/src/main/java/splitstree6/algorithms/splits/splits2report/ShapleyValues.java index 541390c3..d1101bae 100644 --- a/src/main/java/splitstree6/algorithms/splits/splits2report/ShapleyValues.java +++ b/src/main/java/splitstree6/algorithms/splits/splits2report/ShapleyValues.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/splits/splits2splits/BootstrapSplits.java b/src/main/java/splitstree6/algorithms/splits/splits2splits/BootstrapSplits.java index 9ac05330..c73e6327 100755 --- a/src/main/java/splitstree6/algorithms/splits/splits2splits/BootstrapSplits.java +++ b/src/main/java/splitstree6/algorithms/splits/splits2splits/BootstrapSplits.java @@ -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."; } } diff --git a/src/main/java/splitstree6/algorithms/splits/splits2trees/GreedyTree.java b/src/main/java/splitstree6/algorithms/splits/splits2trees/GreedyTree.java index f0490a7b..8eb7db1c 100755 --- a/src/main/java/splitstree6/algorithms/splits/splits2trees/GreedyTree.java +++ b/src/main/java/splitstree6/algorithms/splits/splits2trees/GreedyTree.java @@ -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() { diff --git a/src/main/java/splitstree6/algorithms/trees/trees2distances/AverageDistances.java b/src/main/java/splitstree6/algorithms/trees/trees2distances/AverageDistances.java index 4829da6f..55c04fa1 100755 --- a/src/main/java/splitstree6/algorithms/trees/trees2distances/AverageDistances.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2distances/AverageDistances.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/trees/trees2report/PhylogeneticDiversity.java b/src/main/java/splitstree6/algorithms/trees/trees2report/PhylogeneticDiversity.java index 4eceb958..747f0163 100644 --- a/src/main/java/splitstree6/algorithms/trees/trees2report/PhylogeneticDiversity.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2report/PhylogeneticDiversity.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/trees/trees2report/TreeDiversityIndex.java b/src/main/java/splitstree6/algorithms/trees/trees2report/TreeDiversityIndex.java index a518f91a..e82a59ad 100644 --- a/src/main/java/splitstree6/algorithms/trees/trees2report/TreeDiversityIndex.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2report/TreeDiversityIndex.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/trees/trees2report/UnrootedShapleyValues.java b/src/main/java/splitstree6/algorithms/trees/trees2report/UnrootedShapleyValues.java index dd9325c1..d6bba76e 100644 --- a/src/main/java/splitstree6/algorithms/trees/trees2report/UnrootedShapleyValues.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2report/UnrootedShapleyValues.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/trees/trees2splits/AntiConsensusNetwork.java b/src/main/java/splitstree6/algorithms/trees/trees2splits/AntiConsensusNetwork.java index b55cf965..64275bdf 100755 --- a/src/main/java/splitstree6/algorithms/trees/trees2splits/AntiConsensusNetwork.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2splits/AntiConsensusNetwork.java @@ -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 diff --git a/src/main/java/splitstree6/algorithms/trees/trees2splits/AverageConsensus.java b/src/main/java/splitstree6/algorithms/trees/trees2splits/AverageConsensus.java index 58d5b3de..9ce79d17 100755 --- a/src/main/java/splitstree6/algorithms/trees/trees2splits/AverageConsensus.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2splits/AverageConsensus.java @@ -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() { diff --git a/src/main/java/splitstree6/algorithms/trees/trees2splits/ConsensusNetwork.java b/src/main/java/splitstree6/algorithms/trees/trees2splits/ConsensusNetwork.java index 028164a2..46a8f643 100755 --- a/src/main/java/splitstree6/algorithms/trees/trees2splits/ConsensusNetwork.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2splits/ConsensusNetwork.java @@ -38,7 +38,7 @@ public class ConsensusNetwork extends ConsensusSplits { public String getCitation() { return "Holland et al 2004; BR Holland, KT Huber, V Moulton, and PJ Lockhart." + " Using consensus networks to visualize contradictory evidence for species phylogeny." + - " Molecular Biology and Evolution, 21 (7):1459–1461, 2004 "; + " Molecular Biology and Evolution, 21 (7):1459–1461, 2004."; } @Override diff --git a/src/main/java/splitstree6/algorithms/trees/trees2splits/ConsensusOutline.java b/src/main/java/splitstree6/algorithms/trees/trees2splits/ConsensusOutline.java index 2c3336a1..a54b0cc1 100755 --- a/src/main/java/splitstree6/algorithms/trees/trees2splits/ConsensusOutline.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2splits/ConsensusOutline.java @@ -37,7 +37,7 @@ public class ConsensusOutline extends ConsensusSplits implements IToCircularSplits { @Override public String getCitation() { - return "Huson & Cetinkaya 2023;DH Huson and B Cetinkaya, Visualizing incompatibilities in phylogenetic trees using consensus outlines, Front. Bioinform. (2023) "; + return "Huson & Cetinkaya 2023;DH Huson and B Cetinkaya, Visualizing incompatibilities in phylogenetic trees using consensus outlines, Front. Bioinform, 2023."; } @Override diff --git a/src/main/java/splitstree6/algorithms/trees/trees2splits/ConsensusSplits.java b/src/main/java/splitstree6/algorithms/trees/trees2splits/ConsensusSplits.java index 5ef8741e..eb34f33a 100755 --- a/src/main/java/splitstree6/algorithms/trees/trees2splits/ConsensusSplits.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2splits/ConsensusSplits.java @@ -54,7 +54,7 @@ public enum EdgeWeights {Mean, TreeSizeWeightedMean, Median, Count, Sum, Uniform @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 diff --git a/src/main/java/splitstree6/algorithms/trees/trees2splits/CredibilityNetwork.java b/src/main/java/splitstree6/algorithms/trees/trees2splits/CredibilityNetwork.java index 1a933c33..f5f2c4c0 100755 --- a/src/main/java/splitstree6/algorithms/trees/trees2splits/CredibilityNetwork.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2splits/CredibilityNetwork.java @@ -56,7 +56,7 @@ public class CredibilityNetwork extends Trees2Splits implements DoNotLoadThisAlg public String getCitation() { return "Huson & Bryant 2006; " + "DH Huson and D Bryant. Application of Phylogenetic Networks in Evolutionary Studies. " + - "Mol. Biol. Evol. 23(2):254–267. 2006"; + "Mol. Biol. Evol. 23(2):254–267, 2006."; } @Override diff --git a/src/main/java/splitstree6/algorithms/trees/trees2splits/FilteredSuperNetwork.java b/src/main/java/splitstree6/algorithms/trees/trees2splits/FilteredSuperNetwork.java index d1c81c38..62cf1c55 100644 --- a/src/main/java/splitstree6/algorithms/trees/trees2splits/FilteredSuperNetwork.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2splits/FilteredSuperNetwork.java @@ -51,9 +51,9 @@ public class FilteredSuperNetwork extends SuperNetwork { @Override public String getCitation() { - return "Whitfield et al 2008;JB Whitfield, SA Cameron, DH Huson, MA Steel. " + + return "Whitfield et al 2008;JB Whitfield, SA Cameron, DH Huson and MA Steel. " + "Filtered Z-Closure Supernetworks for Extracting and Visualizing Recurrent Signal from Incongruent Gene Trees, " + - "Systematic Biology, 57(6):939-947 (2008)"; + "Systematic Biology, 57(6):939-947, 2008."; } public List listOptions() { diff --git a/src/main/java/splitstree6/algorithms/trees/trees2splits/SuperNetwork.java b/src/main/java/splitstree6/algorithms/trees/trees2splits/SuperNetwork.java index c2703db0..491b10e8 100755 --- a/src/main/java/splitstree6/algorithms/trees/trees2splits/SuperNetwork.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2splits/SuperNetwork.java @@ -60,7 +60,7 @@ public enum EdgeWeights {AverageRelative, Mean, TreeSizeWeightedMean, Sum, Min, @Override public String getCitation() { return "Huson et al 2004;DH Huson, T. Dezulian, T. Kloepper, and MA Steel. Phylogenetic super-networks from partial trees. " + - "IEEE/ACM Transactions in Computational Biology and Bioinformatics, 1(4):151–158, 2004."; + "IEEE/ACM TCBB, 1(4):151–158, 2004."; } @Override diff --git a/src/main/java/splitstree6/algorithms/trees/trees2trees/ALTSExternal.java b/src/main/java/splitstree6/algorithms/trees/trees2trees/ALTSExternal.java index d0cbe7f5..7aef6d87 100644 --- a/src/main/java/splitstree6/algorithms/trees/trees2trees/ALTSExternal.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2trees/ALTSExternal.java @@ -56,7 +56,7 @@ public class ALTSExternal extends Trees2Trees implements IDesktopOnly { @Override public String getCitation() { return "Zhang et al 2023; L. Zhang, N. Abhari, C. Colijn and Y Wu." + - " A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings. Genome Res. 2023"; + " A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings. Genome Res. 2023."; } @Override diff --git a/src/main/java/splitstree6/algorithms/trees/trees2trees/ALTSNetwork.java b/src/main/java/splitstree6/algorithms/trees/trees2trees/ALTSNetwork.java index 470d7c26..2cf066e1 100644 --- a/src/main/java/splitstree6/algorithms/trees/trees2trees/ALTSNetwork.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2trees/ALTSNetwork.java @@ -53,7 +53,7 @@ public class ALTSNetwork extends Trees2Trees { @Override public String getCitation() { return "Zhang et al 2023; L. Zhang, N. Abhari, C. Colijn and Y Wu." + - " A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings. Genome Res. 2023;" + " A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings. Genome Res. 2023.;" + "Zhang et al 2024; L. Zhang, B. Cetinkaya and DH Huson. Hybridization networks from phylogenetic trees, in preparation."; } diff --git a/src/main/java/splitstree6/algorithms/trees/trees2trees/AutumnAlgorithm.java b/src/main/java/splitstree6/algorithms/trees/trees2trees/AutumnAlgorithm.java index 3f6e18f4..7120630c 100644 --- a/src/main/java/splitstree6/algorithms/trees/trees2trees/AutumnAlgorithm.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2trees/AutumnAlgorithm.java @@ -58,8 +58,8 @@ public String getToolTip(String optionName) { @Override public String getCitation() { - return "Huson & Linz 2018; D.H. Huson and S. Linz. Autumn Algorithm—Computation of Hybridization Networks for Realistic Phylogenetic Trees. " - + "IEEE/ACM Transactions on Computational Biology and Bioinformatics: 15:398-420, 2018."; + return "Huson & Linz 2018; DH Huson and S. Linz. Autumn Algorithm—Computation of Hybridization Networks for Realistic Phylogenetic Trees. " + + "IEEE/ACM TCBB: 15:398-420, 2018."; } @Override diff --git a/src/main/java/splitstree6/algorithms/trees/trees2trees/BootstrapTree.java b/src/main/java/splitstree6/algorithms/trees/trees2trees/BootstrapTree.java index 1a5634e2..23ee610d 100755 --- a/src/main/java/splitstree6/algorithms/trees/trees2trees/BootstrapTree.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2trees/BootstrapTree.java @@ -316,9 +316,9 @@ public void setOptionTransferBootstrap(boolean optionTransferBootstrap) { @Override public String getCitation() { if (!getOptionTransferBootstrap()) - return "Felsenstein 1985;Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39(4):783-791 (1985);"; + return "Felsenstein 1985;J. Felsenstein. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39(4):783-791, 1985.;"; else - return "Lemoine et al 2018;F. Lemoine, JB Entfellner, E. Wilkinson, et al. Renewing Felsenstein’s phylogenetic bootstrap in the era of big data. Nature 556, 452–456 (2018);"; + return "Lemoine et al 2018;F. Lemoine, JB Entfellner, E. Wilkinson, et al. Renewing Felsenstein’s phylogenetic bootstrap in the era of big data. Nature 556, 452–456, 2018."; } } diff --git a/src/main/java/splitstree6/algorithms/trees/trees2trees/ClusterNetwork.java b/src/main/java/splitstree6/algorithms/trees/trees2trees/ClusterNetwork.java index ab23f19d..aea3d839 100755 --- a/src/main/java/splitstree6/algorithms/trees/trees2trees/ClusterNetwork.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2trees/ClusterNetwork.java @@ -72,7 +72,7 @@ public String getToolTip(String optionName) { @Override public String getCitation() { - return "Huson & Rupp 2008; D.H. Huson and R. Rupp (2008) Summarizing multiple gene trees using cluster networks. In: Crandall, K.A., Lagergren, J. (eds) Algorithms in Bioinformatics. WABI 2008. Lecture Notes in Computer Science(), vol 5251."; + return "Huson & Rupp 2008; DH Huson and R. Rupp. Summarizing multiple gene trees using cluster networks. In: KA Crandall and J Lagergren (eds) Algorithms in Bioinformatics. WABI. LNCS, 5251, 2008"; } @Override diff --git a/src/main/java/splitstree6/algorithms/trees/trees2trees/ConsensusTree.java b/src/main/java/splitstree6/algorithms/trees/trees2trees/ConsensusTree.java index 3d5adeb1..0ebb2ae5 100755 --- a/src/main/java/splitstree6/algorithms/trees/trees2trees/ConsensusTree.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2trees/ConsensusTree.java @@ -61,7 +61,7 @@ else if (optionName.equals(optionConsensus.getName())) @Override public String getCitation() { - return "Bryant 2001;D. Bryant, A classification of consensus methods for phylogenetics, in Bioconsensus, 2001"; + return "Bryant 2001;D. Bryant, A classification of consensus methods for phylogenetics, in Bioconsensus, 2001."; } @Override diff --git a/src/main/java/splitstree6/algorithms/trees/trees2trees/Trees2Trees.java b/src/main/java/splitstree6/algorithms/trees/trees2trees/Trees2Trees.java index 10dca7a1..87ab6844 100644 --- a/src/main/java/splitstree6/algorithms/trees/trees2trees/Trees2Trees.java +++ b/src/main/java/splitstree6/algorithms/trees/trees2trees/Trees2Trees.java @@ -210,7 +210,7 @@ public void compute(ProgressListener progress, TaxaBlock taxaBlock, TreesBlock i @Override public String getCitation() { - return "Francis et al, 2021; A Francis, DH Huson and MA Steel. Normalising phylogenetic networks. Molecular Phylogenetics and Evolution, 163 (2021)"; + return "Francis et al, 2021; A Francis, DH Huson and MA Steel. Normalising phylogenetic networks. Molecular Phylogenetics and Evolution, 163, 2021."; } @Override diff --git a/src/main/java/splitstree6/view/trees/densitree/DensiTreeView.java b/src/main/java/splitstree6/view/trees/densitree/DensiTreeView.java index ec12d1b1..020b2427 100644 --- a/src/main/java/splitstree6/view/trees/densitree/DensiTreeView.java +++ b/src/main/java/splitstree6/view/trees/densitree/DensiTreeView.java @@ -234,7 +234,7 @@ public IDisplayTabPresenter getPresenter() { @Override public String getCitation() { - return "Bouckaert 2010; RR Bouckaert. DensiTree: making sense of sets of phylogenetic trees, Bioinformatics 26(1):1372–1373 (2010)"; + return "Bouckaert 2010; RR Bouckaert. DensiTree: making sense of sets of phylogenetic trees, Bioinformatics 26(1):1372–1373, 2010."; } public ViewTab getViewTab() { diff --git a/src/main/java/splitstree6/view/trees/tanglegram/TanglegramView.java b/src/main/java/splitstree6/view/trees/tanglegram/TanglegramView.java index cfb9500e..9514eff6 100644 --- a/src/main/java/splitstree6/view/trees/tanglegram/TanglegramView.java +++ b/src/main/java/splitstree6/view/trees/tanglegram/TanglegramView.java @@ -376,6 +376,6 @@ public int size() { public String getCitation() { return "Scornavacca et al, 2011; " + "C. Scornavacca, F. Zickmann and D.H. Huson. Tanglegrams for rooted phylogenetic trees and networks. " + - "Bioinformatics, 27(13):i248–i256, 2011"; + "Bioinformatics, 27(13):i248–i256, 2011."; } }