data/libpal-java-1.5.1+dfsg/src/build.xml:1: ist ==> is, it, its, it's, sit, list data/libpal-java-1.5.1+dfsg/src/pal/gui/CircularGraphics.java:54: arbitary ==> arbitrary data/libpal-java-1.5.1+dfsg/src/pal/gui/CircularGraphics.java:59: arbitary ==> arbitrary data/libpal-java-1.5.1+dfsg/src/pal/gui/CircularGraphics.java:64: arbitary ==> arbitrary data/libpal-java-1.5.1+dfsg/src/pal/gui/CircularGraphics.java:74: arbitary ==> arbitrary data/libpal-java-1.5.1+dfsg/src/pal/gui/TreePainter.java:123: postions ==> positions data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/GeneralObjectState.java:23: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/GeneralObjectState.java:23: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/GeneralObjectState.java:23: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/UndoableAction.java:16: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/UndoableAction.java:16: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/UndoableAction.java:29: succesful ==> successful data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/UndoableAction.java:76: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/UndoableAction.java:78: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/UndoableAction.java:78: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/UndoableAction.java:79: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/UndoableAction.java:79: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/UndoableAction.java:80: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/UndoableAction.java:95: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/UndoableAction.java:97: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/UndoableAction.java:97: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/UndoableAction.java:98: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/UndoableAction.java:98: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/UndoableAction.java:99: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/ObjectState.java:21: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/algorithmics/ObjectState.java:21: desparate ==> desperate, disparate data/libpal-java-1.5.1+dfsg/src/pal/eval/UnconstrainedLikelihoodModel.java:114: probabilites ==> probabilities data/libpal-java-1.5.1+dfsg/src/pal/eval/LikelihoodValue.java:1291: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/eval/FastLikelihoodCalculator.java:26: accomodate ==> accommodate data/libpal-java-1.5.1+dfsg/src/pal/eval/SimpleLeafCalculator.java:12: probabilites ==> probabilities data/libpal-java-1.5.1+dfsg/src/pal/eval/LikelihoodTool.java:42: choosen ==> chosen data/libpal-java-1.5.1+dfsg/src/pal/eval/LikelihoodTool.java:163: neccessary ==> necessary data/libpal-java-1.5.1+dfsg/src/pal/eval/LHCalculator.java:117: probabilites ==> probabilities data/libpal-java-1.5.1+dfsg/src/pal/eval/LHCalculator.java:183: substituion ==> substitution data/libpal-java-1.5.1+dfsg/src/pal/eval/LikelihoodOptimiser.java:51: acheive ==> achieve data/libpal-java-1.5.1+dfsg/src/pal/eval/LikelihoodOptimiser.java:66: acheive ==> achieve data/libpal-java-1.5.1+dfsg/src/pal/eval/LikelihoodOptimiser.java:80: acheive ==> achieve data/libpal-java-1.5.1+dfsg/src/pal/eval/LikelihoodOptimiser.java:93: acheive ==> achieve data/libpal-java-1.5.1+dfsg/src/pal/eval/LikelihoodOptimiser.java:135: acheive ==> achieve data/libpal-java-1.5.1+dfsg/src/pal/eval/LikelihoodOptimiser.java:149: acheive ==> achieve data/libpal-java-1.5.1+dfsg/src/pal/eval/LikelihoodOptimiser.java:164: acheive ==> achieve data/libpal-java-1.5.1+dfsg/src/pal/eval/ConditionalProbabilityStore.java:66: accomodate ==> accommodate data/libpal-java-1.5.1+dfsg/src/pal/eval/ConditionalProbabilityStore.java:73: accomodate ==> accommodate data/libpal-java-1.5.1+dfsg/src/pal/eval/ConditionalProbabilityStore.java:110: accomodate ==> accommodate data/libpal-java-1.5.1+dfsg/src/pal/eval/ConditionalProbabilityStore.java:122: accomodated ==> accommodated data/libpal-java-1.5.1+dfsg/src/pal/eval/ConditionalProbabilityStore.java:138: accomodate ==> accommodate data/libpal-java-1.5.1+dfsg/src/pal/eval/SimpleLHCalculator.java:413: probabilites ==> probabilities data/libpal-java-1.5.1+dfsg/src/pal/eval/PatternInfo.java:12: upto ==> up to data/libpal-java-1.5.1+dfsg/src/pal/eval/PatternInfo.java:106: mathcing ==> matching data/libpal-java-1.5.1+dfsg/src/pal/coalescent/DemographicClockTree.java:49: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/coalescent/DemographicModel.java:43: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/DemographicModel.java:215: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpConst.java:399: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpConst.java:403: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpConst.java:409: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpConst.java:413: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpConst.java:420: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpConst.java:424: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpConst.java:430: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpConst.java:434: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpConst.java:438: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpConst.java:444: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpConst.java:450: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpConst.java:454: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpConst.java:463: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ExponentialGrowth.java:257: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ExponentialGrowth.java:261: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ExponentialGrowth.java:266: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ExponentialGrowth.java:270: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ExponentialGrowth.java:279: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/CoalescentIntervals.java:66: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/CoalescentIntervals.java:386: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/CoalescentIntervals.java:388: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/CoalescentIntervals.java:405: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpGrowth.java:19: inital ==> initial data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpGrowth.java:497: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpGrowth.java:501: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpGrowth.java:507: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpGrowth.java:511: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpGrowth.java:518: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpGrowth.java:522: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpGrowth.java:528: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpGrowth.java:532: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpGrowth.java:536: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpGrowth.java:542: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpGrowth.java:551: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/SkylinePlot.java:62: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/SkylinePlot.java:167: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/SkylinePlot.java:169: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/SkylinePlot.java:401: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/SkylinePlot.java:407: cummulative ==> cumulative data/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:60: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:61: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:90: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:136: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:137: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:157: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:212: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:215: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:218: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:225: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:230: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:233: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ExpandingPopulation.java:19: inital ==> initial data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ExpandingPopulation.java:244: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ExpandingPopulation.java:248: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ExpandingPopulation.java:254: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ExpandingPopulation.java:258: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ExpandingPopulation.java:264: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ExpandingPopulation.java:268: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ExpandingPopulation.java:275: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ExpandingPopulation.java:282: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstantPopulation.java:200: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstantPopulation.java:205: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstantPopulation.java:210: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstantPopulation.java:219: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/math/MultivariateMinimum.java:148: succesful ==> successful data/libpal-java-1.5.1+dfsg/src/pal/math/DifferentialEvolution.java:49: modul ==> module data/libpal-java-1.5.1+dfsg/src/pal/math/DifferentialEvolution.java:64: modul ==> module data/libpal-java-1.5.1+dfsg/src/pal/math/OrderEnumerator.java:30: differnet ==> different data/libpal-java-1.5.1+dfsg/src/pal/math/OrderEnumerator.java:264: adjusment ==> adjustment data/libpal-java-1.5.1+dfsg/src/pal/math/OrderEnumerator.java:312: adjusment ==> adjustment data/libpal-java-1.5.1+dfsg/src/pal/math/OrderEnumerator.java:350: untill ==> until data/libpal-java-1.5.1+dfsg/src/pal/math/ConjugateDirectionSearch.java:109: vlarge ==> large data/libpal-java-1.5.1+dfsg/src/pal/math/ConjugateDirectionSearch.java:343: vlarge ==> large data/libpal-java-1.5.1+dfsg/src/pal/math/ConjugateDirectionSearch.java:399: vlarge ==> large data/libpal-java-1.5.1+dfsg/src/pal/math/ConjugateDirectionSearch.java:443: vlarge ==> large data/libpal-java-1.5.1+dfsg/src/pal/math/ConjugateDirectionSearch.java:532: vlaue ==> value data/libpal-java-1.5.1+dfsg/src/pal/math/MathUtils.java:37: actaully ==> actually data/libpal-java-1.5.1+dfsg/src/pal/math/OrthogonalHints.java:12: alow ==> allow data/libpal-java-1.5.1+dfsg/src/pal/math/OrthogonalHints.java:53: upto ==> up to data/libpal-java-1.5.1+dfsg/src/pal/math/MersenneTwisterFast.java:94: inforce ==> enforce data/libpal-java-1.5.1+dfsg/src/pal/math/MersenneTwisterFast.java:97: curernt ==> current data/libpal-java-1.5.1+dfsg/src/pal/math/MersenneTwisterFast.java:200: Initalize ==> Initialize data/libpal-java-1.5.1+dfsg/src/pal/math/Matrix.java:102: colums ==> columns data/libpal-java-1.5.1+dfsg/src/pal/math/EvaluationCounter.java:11: utiltity ==> utility data/libpal-java-1.5.1+dfsg/src/pal/math/ConjugateGradientSearch.java:402: sufficent ==> sufficient data/libpal-java-1.5.1+dfsg/src/pal/math/UnivariateMinimum.java:39: neccessary ==> necessary data/libpal-java-1.5.1+dfsg/src/pal/tree/MutationRateModelTree.java:80: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/tree/Local.java:8: Larget ==> Larger, largest, target data/libpal-java-1.5.1+dfsg/src/pal/tree/Local.java:193: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/tree/Local.java:215: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/tree/Local.java:217: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/tree/Local.java:223: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/tree/Local.java:229: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/tree/Local.java:231: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/tree/NodeFactory.java:21: recyle ==> recycle data/libpal-java-1.5.1+dfsg/src/pal/tree/TreeManipulator.java:152: OTU ==> OUT data/libpal-java-1.5.1+dfsg/src/pal/tree/TreeManipulator.java:182: memebers ==> members data/libpal-java-1.5.1+dfsg/src/pal/tree/TreeManipulator.java:537: erro ==> error data/libpal-java-1.5.1+dfsg/src/pal/tree/TreeManipulator.java:654: lenght ==> length data/libpal-java-1.5.1+dfsg/src/pal/tree/TreeManipulator.java:1033: tre ==> tree data/libpal-java-1.5.1+dfsg/src/pal/tree/TreeManipulator.java:1165: orginal ==> original data/libpal-java-1.5.1+dfsg/src/pal/tree/TreeManipulator.java:1550: refered ==> referred data/libpal-java-1.5.1+dfsg/src/pal/tree/TreeManipulator.java:1586: approriate ==> appropriate data/libpal-java-1.5.1+dfsg/src/pal/tree/SplitUtils.java:92: alway ==> always data/libpal-java-1.5.1+dfsg/src/pal/tree/ReadTree.java:101: enountered ==> encountered data/libpal-java-1.5.1+dfsg/src/pal/tree/TreeUtils.java:1168: requrests ==> requests data/libpal-java-1.5.1+dfsg/src/pal/tree/ClockTree.java:49: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/tree/NodeUtils.java:89: maxium ==> maximum data/libpal-java-1.5.1+dfsg/src/pal/tree/NodeUtils.java:388: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/tree/NodeUtils.java:389: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/tree/NodeUtils.java:428: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/tree/NodeUtils.java:444: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/tree/TreeTool.java:105: choosen ==> chosen data/libpal-java-1.5.1+dfsg/src/pal/tree/ParameterizedTree.java:42: implment ==> implement data/libpal-java-1.5.1+dfsg/src/pal/tree/UnconstrainedTree.java:41: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/tree/ClusterTree.java:11: Complet ==> Complete data/libpal-java-1.5.1+dfsg/src/pal/tree/ClusterTree.java:114: swaped ==> swapped data/libpal-java-1.5.1+dfsg/src/pal/distance/DistanceMatrixUtils.java:16: Auxillary ==> Auxiliary data/libpal-java-1.5.1+dfsg/src/pal/supgma/SUPGMABase.java:466: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/supgma/SUPGMABase.java:467: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/supgma/SUPGMABase.java:468: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/supgma/RateHandler.java:34: arbitary ==> arbitrary data/libpal-java-1.5.1+dfsg/src/pal/supgma/RateHandler.java:183: arbitary ==> arbitrary data/libpal-java-1.5.1+dfsg/src/pal/treesearch/FreeBranch.java:108: retreival ==> retrieval data/libpal-java-1.5.1+dfsg/src/pal/treesearch/FreeBranch.java:271: inconsitent ==> inconsistent data/libpal-java-1.5.1+dfsg/src/pal/treesearch/TreeSearchTool.java:32: OTU ==> OUT data/libpal-java-1.5.1+dfsg/src/pal/treesearch/TreeSearchTool.java:33: choosen ==> chosen data/libpal-java-1.5.1+dfsg/src/pal/treesearch/TreeSearchTool.java:44: OTU ==> OUT data/libpal-java-1.5.1+dfsg/src/pal/treesearch/TreeSearchTool.java:45: choosen ==> chosen data/libpal-java-1.5.1+dfsg/src/pal/treesearch/TreeSearchTool.java:59: OTU ==> OUT data/libpal-java-1.5.1+dfsg/src/pal/treesearch/TreeSearchTool.java:60: choosen ==> chosen data/libpal-java-1.5.1+dfsg/src/pal/treesearch/TreeSearchTool.java:70: OTU ==> OUT data/libpal-java-1.5.1+dfsg/src/pal/treesearch/TreeSearchTool.java:71: choosen ==> chosen data/libpal-java-1.5.1+dfsg/src/pal/treesearch/TreeSearchTool.java:87: choosen ==> chosen data/libpal-java-1.5.1+dfsg/src/pal/treesearch/TreeSearchTool.java:101: choosen ==> chosen data/libpal-java-1.5.1+dfsg/src/pal/treesearch/TreeSearchTool.java:134: contraints ==> constraints data/libpal-java-1.5.1+dfsg/src/pal/treesearch/TreeSearchTool.java:138: choosen ==> chosen data/libpal-java-1.5.1+dfsg/src/pal/treesearch/TreeSearchTool.java:218: neccessary ==> necessary data/libpal-java-1.5.1+dfsg/src/pal/treesearch/AbstractParentableConstrainedNode.java:95: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/treesearch/ConstrainedNode.java:25: minum ==> minimum data/libpal-java-1.5.1+dfsg/src/pal/treesearch/GeneralConstructionTool.java:175: OTU ==> OUT data/libpal-java-1.5.1+dfsg/src/pal/treesearch/GeneralConstructionTool.java:176: OTU ==> OUT data/libpal-java-1.5.1+dfsg/src/pal/treesearch/GeneralConstructionTool.java:178: OTU ==> OUT data/libpal-java-1.5.1+dfsg/src/pal/treesearch/GeneralOptimisable.java:26: occured ==> occurred data/libpal-java-1.5.1+dfsg/src/pal/treesearch/ConstrainedLeafNode.java:101: childs ==> children, child's data/libpal-java-1.5.1+dfsg/src/pal/treesearch/SRDTGlobalClockModel.java:128: infered ==> inferred data/libpal-java-1.5.1+dfsg/src/pal/treesearch/BranchAccess.java:70: arbitary ==> arbitrary data/libpal-java-1.5.1+dfsg/src/pal/treesearch/BranchAccess.java:76: arbitary ==> arbitrary data/libpal-java-1.5.1+dfsg/src/pal/treesearch/BranchAccess.java:120: interesection ==> intersection data/libpal-java-1.5.1+dfsg/src/pal/treesearch/BranchAccess.java:126: interesection ==> intersection data/libpal-java-1.5.1+dfsg/src/pal/treesearch/BranchAccess.java:142: desination ==> destination data/libpal-java-1.5.1+dfsg/src/pal/treesearch/BranchAccess.java:143: desination ==> destination data/libpal-java-1.5.1+dfsg/src/pal/treesearch/BranchAccess.java:145: desination ==> destination data/libpal-java-1.5.1+dfsg/src/pal/treesearch/BranchAccess.java:146: desination ==> destination data/libpal-java-1.5.1+dfsg/src/pal/treesearch/BranchAccess.java:147: desination ==> destination data/libpal-java-1.5.1+dfsg/src/pal/treesearch/BranchAccess.java:148: desination ==> destination data/libpal-java-1.5.1+dfsg/src/pal/treesearch/GeneralLikelihoodSearcher.java:188: heirachy ==> hierarchy data/libpal-java-1.5.1+dfsg/src/pal/treesearch/FreeNode.java:66: redunant ==> redundant data/libpal-java-1.5.1+dfsg/src/pal/treesearch/MRDTGlobalClockModel.java:144: infered ==> inferred data/libpal-java-1.5.1+dfsg/src/pal/treesearch/UnrootedMLSearcher.java:57: OTU ==> OUT data/libpal-java-1.5.1+dfsg/src/pal/treesearch/UnrootedMLSearcher.java:190: Simulataneous ==> Simultaneous data/libpal-java-1.5.1+dfsg/src/pal/treesearch/UnrootedMLSearcher.java:910: Peform ==> Perform data/libpal-java-1.5.1+dfsg/src/pal/treesearch/UnrootedMLSearcher.java:1057: redunant ==> redundant data/libpal-java-1.5.1+dfsg/src/pal/treesearch/UnrootedMLSearcher.java:1153: comming ==> coming data/libpal-java-1.5.1+dfsg/src/pal/treesearch/UnrootedMLSearcher.java:1174: comming ==> coming data/libpal-java-1.5.1+dfsg/src/pal/treesearch/UnrootedMLSearcher.java:1224: orginal ==> original data/libpal-java-1.5.1+dfsg/src/pal/treesearch/UnrootedMLSearcher.java:1275: orginal ==> original data/libpal-java-1.5.1+dfsg/src/pal/treesearch/UnrootedMLSearcher.java:1276: orginal ==> original data/libpal-java-1.5.1+dfsg/src/pal/treesearch/UnrootedMLSearcher.java:1785: Uknown ==> Unknown data/libpal-java-1.5.1+dfsg/src/pal/treesearch/UnrootedMLSearcher.java:2152: retreival ==> retrieval data/libpal-java-1.5.1+dfsg/src/pal/treesearch/UnrootedMLSearcher.java:2334: inconsitent ==> inconsistent data/libpal-java-1.5.1+dfsg/src/pal/substmodel/AbstractRateMatrix.java:419: acheive ==> achieve data/libpal-java-1.5.1+dfsg/src/pal/substmodel/Dayhoff.java:20: Structur ==> Structure data/libpal-java-1.5.1+dfsg/src/pal/substmodel/Dayhoff.java:89: Structur ==> Structure data/libpal-java-1.5.1+dfsg/src/pal/substmodel/YangCodonModel.java:337: implment ==> implement data/libpal-java-1.5.1+dfsg/src/pal/substmodel/YangCodonModel.java:598: implment ==> implement data/libpal-java-1.5.1+dfsg/src/pal/substmodel/YangCodonModel.java:600: repectively ==> respectively data/libpal-java-1.5.1+dfsg/src/pal/substmodel/GeneralREVRateMatrix.java:22: arbitarily ==> arbitrarily data/libpal-java-1.5.1+dfsg/src/pal/substmodel/GeneralREVRateMatrix.java:63: contraints ==> constraints data/libpal-java-1.5.1+dfsg/src/pal/substmodel/GeneralREVRateMatrix.java:81: contraints ==> constraints data/libpal-java-1.5.1+dfsg/src/pal/substmodel/GeneralREVRateMatrix.java:100: contraints ==> constraints data/libpal-java-1.5.1+dfsg/src/pal/substmodel/SubstitutionModel.java:33: probabilites ==> probabilities data/libpal-java-1.5.1+dfsg/src/pal/substmodel/SubstitutionModel.java:108: modle ==> model data/libpal-java-1.5.1+dfsg/src/pal/substmodel/MultiRateMatrixHandler.java:233: acheive ==> achieve data/libpal-java-1.5.1+dfsg/src/pal/substmodel/RateMatrixHandler.java:151: acheive ==> achieve data/libpal-java-1.5.1+dfsg/src/pal/datatype/SpecificAminoAcids.java:13: specifiy ==> specify data/libpal-java-1.5.1+dfsg/src/pal/datatype/DataType.java:171: implmenting ==> implementing data/libpal-java-1.5.1+dfsg/src/pal/datatype/DataType.java:226: prefered ==> preferred data/libpal-java-1.5.1+dfsg/src/pal/datatype/DataType.java:246: prefered ==> preferred data/libpal-java-1.5.1+dfsg/src/pal/datatype/DataType.java:247: prefered ==> preferred data/libpal-java-1.5.1+dfsg/src/pal/datatype/DataType.java:388: beggining ==> beginning data/libpal-java-1.5.1+dfsg/src/pal/datatype/CodonTableFactory.java:54: Ser ==> Set data/libpal-java-1.5.1+dfsg/src/pal/datatype/CodonTableFactory.java:65: Ser ==> Set data/libpal-java-1.5.1+dfsg/src/pal/datatype/CodonTableFactory.java:92: Ser ==> Set data/libpal-java-1.5.1+dfsg/src/pal/datatype/CodonTableFactory.java:176: ment ==> meant data/libpal-java-1.5.1+dfsg/src/pal/datatype/CodonTableFactory.java:364: Ser ==> Set data/libpal-java-1.5.1+dfsg/src/pal/datatype/CodonTableFactory.java:412: Ser ==> Set data/libpal-java-1.5.1+dfsg/src/pal/datatype/SimpleDataType.java:79: overidden ==> overridden data/libpal-java-1.5.1+dfsg/src/pal/datatype/SimpleDataType.java:80: get's ==> gets data/libpal-java-1.5.1+dfsg/src/pal/datatype/SimpleDataType.java:80: get's ==> gets data/libpal-java-1.5.1+dfsg/src/pal/datatype/SimpleDataType.java:96: retrun ==> return data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACNucleotides.java:79: retrun ==> return data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACNucleotides.java:273: arbitary ==> arbitrary data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACNucleotides.java:282: arbitary ==> arbitrary data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACNucleotides.java:283: orignal ==> original data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACNucleotides.java:299: arbitary ==> arbitrary data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACNucleotides.java:301: orignal ==> original data/libpal-java-1.5.1+dfsg/src/pal/datatype/AminoAcids.java:41: SER ==> SET data/libpal-java-1.5.1+dfsg/src/pal/datatype/AminoAcids.java:155: retrun ==> return data/libpal-java-1.5.1+dfsg/src/pal/datatype/GapBalanced.java:28: becuase ==> because data/libpal-java-1.5.1+dfsg/src/pal/datatype/GapBalanced.java:146: retrun ==> return data/libpal-java-1.5.1+dfsg/src/pal/datatype/Codons.java:95: retrun ==> return data/libpal-java-1.5.1+dfsg/src/pal/datatype/TwoStates.java:49: retrun ==> return data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:27: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:32: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:33: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:34: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:35: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:37: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:37: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:37: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:37: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:37: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:38: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:38: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:38: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:38: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:38: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:39: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:39: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:39: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:39: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:39: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:40: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:40: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:40: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:40: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:40: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:41: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:41: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:41: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:41: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:41: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:42: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:42: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:42: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:42: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:42: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:44: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:45: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:46: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:47: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:49: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:49: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:49: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:49: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:49: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:49: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:49: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:49: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:49: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:49: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:49: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:49: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:49: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:49: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACPenaltyTable.java:49: thq ==> the data/libpal-java-1.5.1+dfsg/src/pal/datatype/StateRemover.java:56: retrun ==> return data/libpal-java-1.5.1+dfsg/src/pal/statistics/ReplicateLikelihoodEvaluator.java:26: subtitution ==> substitution data/libpal-java-1.5.1+dfsg/src/pal/statistics/ShimodairaHasegawaTest.java:82: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/statistics/ShimodairaHasegawaTest.java:91: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/statistics/ShimodairaHasegawaTest.java:93: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/statistics/KishinoHasegawaTest.java:78: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/statistics/KishinoHasegawaTest.java:86: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/statistics/KishinoHasegawaTest.java:88: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/statistics/KishinoHasegawaTest.java:90: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/statistics/ContigencyTable.java:147: slighly ==> slightly data/libpal-java-1.5.1+dfsg/src/pal/statistics/ContigencyTable.java:200: slighly ==> slightly data/libpal-java-1.5.1+dfsg/src/pal/statistics/ModelSupport.java:94: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/statistics/ModelSupport.java:104: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/statistics/ModelSupport.java:106: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/statistics/ModelSupport.java:108: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/statistics/ModelSupport.java:136: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/statistics/ModelSupport.java:157: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/popgen/LinkageDisequilibrium.java:194: countR ==> counter, contour, country, county data/libpal-java-1.5.1+dfsg/src/pal/popgen/LinkageDisequilibrium.java:196: countR ==> counter, contour, country, county data/libpal-java-1.5.1+dfsg/src/pal/popgen/LinkageDisequilibrium.java:341: aligment ==> alignment data/libpal-java-1.5.1+dfsg/src/pal/io/NexusTokenizer.java:336: saftey ==> safety data/libpal-java-1.5.1+dfsg/src/pal/misc/PalEventMulticaster.java:11: accomodating ==> accommodating data/libpal-java-1.5.1+dfsg/src/pal/misc/Parameterized.java:161: refected ==> reflected data/libpal-java-1.5.1+dfsg/src/pal/misc/Parameterized.java:174: refected ==> reflected data/libpal-java-1.5.1+dfsg/src/pal/misc/Parameterized.java:189: refected ==> reflected data/libpal-java-1.5.1+dfsg/src/pal/misc/Parameterized.java:249: paramters ==> parameters data/libpal-java-1.5.1+dfsg/src/pal/misc/Parameterized.java:268: paramters ==> parameters data/libpal-java-1.5.1+dfsg/src/pal/misc/ParameterizedDoubleBundle.java:12: changable ==> changeable data/libpal-java-1.5.1+dfsg/src/pal/misc/Utils.java:233: formating ==> formatting data/libpal-java-1.5.1+dfsg/src/pal/misc/Utils.java:248: formating ==> formatting data/libpal-java-1.5.1+dfsg/src/pal/misc/Utils.java:262: formating ==> formatting data/libpal-java-1.5.1+dfsg/src/pal/misc/Utils.java:271: formating ==> formatting data/libpal-java-1.5.1+dfsg/src/pal/misc/Utils.java:287: formating ==> formatting data/libpal-java-1.5.1+dfsg/src/pal/misc/Utils.java:295: formating ==> formatting data/libpal-java-1.5.1+dfsg/src/pal/misc/Utils.java:303: formating ==> formatting data/libpal-java-1.5.1+dfsg/src/pal/misc/Utils.java:320: formating ==> formatting data/libpal-java-1.5.1+dfsg/src/pal/misc/Utils.java:332: formating ==> formatting data/libpal-java-1.5.1+dfsg/src/pal/misc/SimpleSummarizable.java:33: immitating ==> imitating data/libpal-java-1.5.1+dfsg/src/pal/misc/TimeOrderCharacterData.java:227: memebers ==> members data/libpal-java-1.5.1+dfsg/src/pal/misc/TimeOrderCharacterData.java:636: guarranteed ==> guaranteed data/libpal-java-1.5.1+dfsg/src/pal/misc/TimeOrderCharacterData.java:637: differenct ==> different data/libpal-java-1.5.1+dfsg/src/pal/misc/TimeOrderCharacterData.java:638: differenct ==> different data/libpal-java-1.5.1+dfsg/src/pal/mep/WindowedMutationRate.java:312: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/mep/WindowedMutationRate.java:314: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/mep/WindowedMutationRate.java:317: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/mep/WindowedMutationRate.java:320: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/mep/ConstantMutationRate.java:234: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/mep/MutationRateModel.java:36: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/mep/MutationRateModel.java:62: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/mep/MutationRateModel.java:72: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/mep/MutationRateModel.java:77: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/mep/MutationRateModel.java:180: Overide ==> Override data/libpal-java-1.5.1+dfsg/src/pal/mep/SteppedMutationRate.java:92: excpected ==> expected data/libpal-java-1.5.1+dfsg/src/pal/mep/SteppedMutationRate.java:102: excpected ==> expected data/libpal-java-1.5.1+dfsg/src/pal/mep/SteppedMutationRate.java:359: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/mep/SteppedMutationRate.java:362: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/mep/SteppedMutationRate.java:366: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/mep/SteppedMutationRate.java:369: fo ==> of, for data/libpal-java-1.5.1+dfsg/src/pal/alignment/AlignmentUtils.java:24: construtors ==> constructors data/libpal-java-1.5.1+dfsg/src/pal/alignment/AlignmentUtils.java:24: refered ==> referred data/libpal-java-1.5.1+dfsg/src/pal/alignment/AlignmentUtils.java:357: frequences ==> frequencies data/libpal-java-1.5.1+dfsg/src/pal/alignment/AlignmentUtils.java:357: frequences ==> frequencies data/libpal-java-1.5.1+dfsg/src/pal/alignment/AlignmentUtils.java:368: frequences ==> frequencies data/libpal-java-1.5.1+dfsg/src/pal/alignment/AlignmentUtils.java:368: frequences ==> frequencies data/libpal-java-1.5.1+dfsg/src/pal/alignment/ReadAlignmentOld.java:115: beggining ==> beginning data/libpal-java-1.5.1+dfsg/src/pal/alignment/SimpleAnnotatedAlignment.java:173: thes ==> this, these data/libpal-java-1.5.1+dfsg/src/pal/alignment/MultiLocusAnnotatedAlignment.java:154: thes ==> this, these data/libpal-java-1.5.1+dfsg/src/pal/alignment/GapBalancedAlignment.java:189: Proccess ==> Process data/libpal-java-1.5.1+dfsg/src/pal/alignment/AlignmentReaders.java:127: toWords ==> towards data/libpal-java-1.5.1+dfsg/src/pal/alignment/AlignmentReaders.java:151: toWords ==> towards data/libpal-java-1.5.1+dfsg/src/pal/alignment/AlignmentReaders.java:275: cound ==> could, count data/libpal-java-1.5.1+dfsg/src/pal/alignment/AlignmentReaders.java:394: toWords ==> towards data/libpal-java-1.5.1+dfsg/src/pal/alignment/SitePattern.java:110: Suh ==> Such data/libpal-java-1.5.1+dfsg/src/pal/alignment/SitePattern.java:266: alighnment ==> alignment data/libpal-java-1.5.1+dfsg/src/pal/util/HeapSort.java:129: orignal ==> original data/libpal-java-1.5.1+dfsg/src/pal/util/HeapSort.java:161: ingoring ==> ignoring data/libpal-java-1.5.1+dfsg/src/pal/util/Comparator.java:14: superceded ==> superseded data/libpal-java-1.5.1+dfsg/src/pal/util/Comparable.java:13: superceded ==> superseded data/libpal-java-1.5.1+dfsg/src/pal/util/AlgorithmCallback.java:13: intergrated ==> integrated data/libpal-java-1.5.1+dfsg/doc/download.html:79: comming ==> coming data/libpal-java-1.5.1+dfsg/doc/download.html:80: comming ==> coming data/libpal-java-1.5.1+dfsg/doc/download.html:81: slighty ==> slightly data/libpal-java-1.5.1+dfsg/doc/history.html:68: Substatial ==> Substantial data/libpal-java-1.5.1+dfsg/doc/history.html:73: managment ==> management data/libpal-java-1.5.1+dfsg/doc/online.html:64: Comming ==> Coming data/libpal-java-1.5.1+dfsg/doc/user_interfaces.html:74: MSDOS ==> MS-DOS data/libpal-java-1.5.1+dfsg/debian/changelog:8: fo ==> of, for