Index

A

ABC (class in egglib.egglib_binding) add() (egglib.fitmodel.Dataset method) (egglib.fitmodel.PriorDiscrete method) (egglib.fitmodel.PriorDumb method) add_feature() (egglib.GenBank method) add_fname() (egglib.egglib_binding.ABC method) add_model() (in module egglib.fitmodel) add_node() (egglib.Tree method) add_qualifier() (egglib.GenBankFeature method) add_son() (egglib.TreeNode method) addBaseChoice() (egglib.GenBankFeatureLocation method) addBaseRange() (egglib.GenBankFeatureLocation method) addBetweenBase() (egglib.GenBankFeatureLocation method) addChange() (egglib.egglib_binding.ParamSet method) addPopulation() (egglib.egglib_binding.Current method) (egglib.egglib_binding.ParamSet method) addSequences() (egglib.Align method) (egglib.Container method) addSingleBase() (egglib.GenBankFeatureLocation method) addTime() (egglib.egglib_binding.Arg method) ageMRCA() (egglib.egglib_binding.Arg method) ageUltimateMRCA() (egglib.egglib_binding.Arg method) Align (class in egglib) (class in egglib.egglib_binding) align() (egglib.egglib_binding.Convert static method)

all_leaves() (egglib.Tree method) allele() (egglib.egglib_binding.SitePolymorphism method) alleleFrequency() (egglib.egglib_binding.SitePolymorphism method) alleleFrequencyPerPopulation() (egglib.egglib_binding.FStatistics method) (egglib.egglib_binding.HFStatistics method) alleleFrequencyTotal() (egglib.egglib_binding.FStatistics method) (egglib.egglib_binding.HFStatistics method) alleleValue() (egglib.egglib_binding.FStatistics method) (egglib.egglib_binding.HFStatistics method) AllMigrationRateChange (class in egglib.egglib_binding) AllPopulationSizeChange (class in egglib.egglib_binding) aln2fas() (in module egglib.tools) AM (class in egglib.fitmodel) ambiguousPositions() (egglib.egglib_binding.Consensus method) append() (egglib.Align method) (egglib.Container method) (egglib.egglib_binding.Align method) (egglib.egglib_binding.Container method) appendSequence() (egglib.Align method) (egglib.Container method) (egglib.egglib_binding.Align method) (egglib.egglib_binding.Container method) apply() (egglib.egglib_binding.AllMigrationRateChange method) (egglib.egglib_binding.AllPopulationSizeChange method) (egglib.egglib_binding.Bottleneck method) (egglib.egglib_binding.Change method) (egglib.egglib_binding.GrowthRateChange method) (egglib.egglib_binding.PopulationBottleneck method) (egglib.egglib_binding.PopulationFusion method) (egglib.egglib_binding.PopulationGrowthRateChange method) (egglib.egglib_binding.PopulationParamChange method) (egglib.egglib_binding.PopulationSplit method) (egglib.egglib_binding.SelfingRateChange method) (egglib.egglib_binding.SingleMigrationRateChange method) (egglib.egglib_binding.SingleParamChange method) (egglib.egglib_binding.SinglePopulationSizeChange method) Arg (class in egglib.egglib_binding) ascendants() (egglib.TreeNode method) asOrder() (egglib.GenBankFeatureLocation method) asRange() (egglib.GenBankFeatureLocation method) atLeastPartiallyResolvedAmbiguities() (egglib.egglib_binding.Consensus method) average_Pi() (egglib.egglib_binding.NucleotideDiversity method)

B

backalign() (in module egglib.tools) BaseCommand (class in egglib.utils) BaseDiversity (class in egglib.egglib_binding) binSwitch() (egglib.Align method) (egglib.egglib_binding.Align method) BL2SEQ (class in egglib.wrappers) BLAST (class in egglib.wrappers) BLASTdb (class in egglib.wrappers) blastn() (egglib.wrappers.BL2SEQ method) (egglib.wrappers.BLAST method) blastp() (egglib.wrappers.BL2SEQ method) (egglib.wrappers.BLAST method)

blastx() (egglib.wrappers.BL2SEQ method) (egglib.wrappers.BLAST method) BNM (class in egglib.fitmodel) Bottleneck (class in egglib.egglib_binding) bottleneck() (egglib.egglib_binding.Controller method) (egglib.simul.CoalesceParamSet method) bottom (egglib.egglib_binding.Edge attribute) BppDiversity (class in egglib.egglib_binding) branch_from() (egglib.TreeNode method) branch_to() (egglib.TreeNode method) brief (egglib.utils.BaseCommand attribute)

C

Change (class in egglib.egglib_binding) changeAllGrowthRates() (egglib.simul.CoalesceParamSet method) changeAllMigrationRates() (egglib.simul.CoalesceParamSet method) changeAllPopulationSizes() (egglib.simul.CoalesceParamSet method) changePairwiseMigrationRate() (egglib.simul.CoalesceParamSet method) changeSelfingRate() (egglib.simul.CoalesceParamSet method) changeSinglePopulationGrowthRate() (egglib.simul.CoalesceParamSet method) changeSinglePopulationSize() (egglib.simul.CoalesceParamSet method) character() (egglib.Align method) (egglib.egglib_binding.Align method) (egglib.egglib_binding.CharMatrix method) (egglib.egglib_binding.DataMatrix method) CharMatrix (class in egglib.egglib_binding) check_pairs() (egglib.wrappers.Primer3 method) check_sequences() (egglib.egglib_binding.Consensus method) chisquare() (in module egglib.tools) clean_edge_lengths() (egglib.Tree method) clean_internal_labels() (egglib.Tree method) clean_pair_ends() (egglib.wrappers.Primer3 method) clean_primer_ends() (egglib.wrappers.Primer3 method) clear() (egglib.Align method) (egglib.Container method) (egglib.SSR method) (egglib.egglib_binding.Align method) (egglib.egglib_binding.Container method) (egglib.egglib_binding.DataMatrix method) (egglib.fitmodel.PriorDiscrete method) (egglib.fitmodel.PriorDumb method) close() (egglib.tools.Updater method) closed (egglib.tools.Updater attribute) clustal() (in module egglib.wrappers) coalesce() (in module egglib.simul) CoalesceFiniteAlleleMutator (class in egglib.simul) CoalesceInfiniteAlleleMutator (class in egglib.simul) CoalesceMutator (class in egglib.simul) coalescence() (egglib.egglib_binding.Arg method) (egglib.egglib_binding.Edge method) CoalesceParamSet (class in egglib.simul)

CoalesceStepwiseMutator (class in egglib.simul) CoalesceTwoPhaseMutator (class in egglib.simul) Codeml (class in egglib.wrappers) codes() (egglib.tools.GeneticCodes class method) codon() (egglib.tools.ReadingFrame method) codons() (egglib.tools.ReadingFrame method) collapse() (egglib.Tree method) column() (egglib.Align method) CommonAlleles() (egglib.egglib_binding.NucleotideDiversity method) compare() (in module egglib.tools) complementaryPositions() (egglib.egglib_binding.Consensus method) composition() (egglib.Align method) (egglib.Container method) concat() (in module egglib.tools) config() (egglib.fitmodel.Dataset method) connect() (egglib.TreeNode method) Consensus (class in egglib.egglib_binding) consensus() (egglib.Align method) (egglib.egglib_binding.Consensus method) consistentPositions() (egglib.egglib_binding.Consensus method) Container (class in egglib) (class in egglib.egglib_binding) contains_duplicates() (egglib.Align method) (egglib.Container method) Controller (class in egglib.egglib_binding) Convert (class in egglib.egglib_binding) copy() (egglib.GenBankFeature method) (egglib.GenBankFeatureLocation method) (egglib.Tree method) correl() (egglib.egglib_binding.LinkageDisequilibrium method) (in module egglib.tools) coverage (egglib.egglib_binding.Edge attribute) create() (egglib.Align class method) (egglib.Container class method) Current (class in egglib.egglib_binding)

D

D() (egglib.egglib_binding.BppDiversity method) d() (egglib.egglib_binding.LinkageDisequilibrium method) D() (egglib.egglib_binding.LinkageDisequilibrium method) (egglib.egglib_binding.NucleotideDiversity method) DataMatrix (class in egglib.egglib_binding) dataMatrix() (egglib.Align method) Dataset (class in egglib.fitmodel) date() (egglib.egglib_binding.AllMigrationRateChange method) (egglib.egglib_binding.AllPopulationSizeChange method) (egglib.egglib_binding.Bottleneck method) (egglib.egglib_binding.Change method) (egglib.egglib_binding.GrowthRateChange method) (egglib.egglib_binding.PopulationBottleneck method) (egglib.egglib_binding.PopulationFusion method) (egglib.egglib_binding.PopulationGrowthRateChange method) (egglib.egglib_binding.PopulationParamChange method) (egglib.egglib_binding.PopulationSplit method) (egglib.egglib_binding.SelfingRateChange method) (egglib.egglib_binding.SingleMigrationRateChange method) (egglib.egglib_binding.SingleParamChange method) (egglib.egglib_binding.SinglePopulationSizeChange method) dateOfLastChange() (egglib.egglib_binding.ParamSet method) daughter() (egglib.egglib_binding.PopulationFusion method) debug (egglib.utils.BaseCommand attribute) default_parameters (egglib.wrappers.Primer3 attribute) derivedAlleleFrequency() (egglib.egglib_binding.SitePolymorphism method)

descendants() (egglib.TreeNode method) description (egglib.utils.BaseCommand attribute) dest() (egglib.egglib_binding.SingleMigrationRateChange method) Deta() (egglib.egglib_binding.BppDiversity method) Dfl() (egglib.egglib_binding.BppDiversity method) Dflstar() (egglib.egglib_binding.BppDiversity method) DOM (class in egglib.fitmodel) doubles() (egglib.egglib_binding.ParamSet method) Dp() (egglib.egglib_binding.LinkageDisequilibrium method) draw() (egglib.fitmodel.PriorDiscrete method) (egglib.fitmodel.PriorDumb method) duplicates() (egglib.Align method) (egglib.Container method)

E

E() (egglib.egglib_binding.NucleotideDiversity method) Edge (class in egglib.egglib_binding) egglib.fitmodel (module) egglib.simul (module) egglib.test (module) egglib.tools (module) egglib.utils (module) egglib.wrappers (module)

encode() (egglib.Align method) (egglib.Container method) equalize() (egglib.Container method) (egglib.egglib_binding.Align method) (egglib.egglib_binding.Container method) erand() (egglib.egglib_binding.Random method) eta() (egglib.egglib_binding.BppDiversity method) (egglib.egglib_binding.NucleotideDiversity method) execute() (in module egglib.utils) exon() (egglib.tools.ReadingFrame method) extract() (egglib.Align method) (egglib.GenBank method) (egglib.TIGR method)

F

F() (egglib.egglib_binding.BppDiversity method) f() (egglib.egglib_binding.FStatistics method) F() (egglib.egglib_binding.FStatistics method) Fasta (class in egglib.egglib_binding) filter() (egglib.Align method) find() (egglib.Align method) (egglib.Container method) (egglib.egglib_binding.Align method) (egglib.egglib_binding.Container method) find_pairs() (egglib.wrappers.Primer3 method) find_primers() (egglib.wrappers.Primer3 method) findGroup() (egglib.Tree method) findMonophyleticGroup() (egglib.Tree method) firstSequenceNames() (egglib.egglib_binding.Consensus method) fit() (egglib.wrappers.Codeml method) fix_gap_ends() (egglib.Align method) fix_omega() (egglib.wrappers.Codeml method)

FixedDifferences() (egglib.egglib_binding.NucleotideDiversity method) fixedNumberOfMutation() (egglib.simul.CoalesceFiniteAlleleMutator method) (egglib.simul.CoalesceInfiniteAlleleMutator method) (egglib.simul.CoalesceMutator method) (egglib.simul.CoalesceStepwiseMutator method) (egglib.simul.CoalesceTwoPhaseMutator method) fixedNumberOfMutations() (egglib.egglib_binding.Mutator method) flags (egglib.utils.BaseCommand attribute) force_positive() (egglib.fitmodel.PriorDiscrete method) (egglib.fitmodel.PriorDumb method) format() (egglib.egglib_binding.Fasta static method) (egglib.egglib_binding.Ms static method) (egglib.tools.Updater method) formatf() (egglib.egglib_binding.Fasta static method) forward_primers() (egglib.wrappers.Primer3 method) frequency_nodes() (egglib.Tree method) Fst() (egglib.egglib_binding.HaplotypeDiversity method) Fstar() (egglib.egglib_binding.BppDiversity method) FStatistics (class in egglib.egglib_binding) Fstats() (egglib.SSR method)

G

GDB (class in egglib.fitmodel) genalys2fasta() (in module egglib.tools) GenBank (class in egglib) GenBankFeature (class in egglib) GenBankFeatureLocation (class in egglib) generate() (egglib.fitmodel.AM method) (egglib.fitmodel.BNM method) (egglib.fitmodel.DOM method) (egglib.fitmodel.GDB method) (egglib.fitmodel.GGDB method) (egglib.fitmodel.IM method) (egglib.fitmodel.IMG method) (egglib.fitmodel.IMiG method) (egglib.fitmodel.IMiGn method) (egglib.fitmodel.IMn method) (egglib.fitmodel.MRC method) (egglib.fitmodel.PEM method) (egglib.fitmodel.SM method) (egglib.fitmodel.SNM method) GeneticCodes (class in egglib.tools) genotypeFrequencyPerPopulation() (egglib.egglib_binding.FStatistics method) genotypeFrequencyTotal() (egglib.egglib_binding.FStatistics method) get() (egglib.Align method) (egglib.Container method) (egglib.egglib_binding.Align method) (egglib.egglib_binding.Container method) (egglib.egglib_binding.DataMatrix method) (egglib.egglib_binding.Ms static method) get_fgenesh() (in module egglib.tools) get_label() (egglib.TreeNode method) get_node() (egglib.Tree method) get_node_re() (egglib.Tree method) get_nodes() (egglib.Tree method) get_nodes_re() (egglib.Tree method)

get_position() (egglib.egglib_binding.BaseDiversity method) (egglib.egglib_binding.HaplotypeDiversity method) (egglib.egglib_binding.LinkageDisequilibrium method) (egglib.egglib_binding.NucleotideDiversity method) get_sequence() (egglib.GenBank method) (egglib.GenBankFeature method) get_site() (egglib.egglib_binding.BaseDiversity method) (egglib.egglib_binding.HaplotypeDiversity method) (egglib.egglib_binding.LinkageDisequilibrium method) (egglib.egglib_binding.NucleotideDiversity method) get_terminal_nodes() (egglib.Tree method) get_threshold() (egglib.egglib_binding.ABC method) getArg() (egglib.egglib_binding.Controller method) GGDB (class in egglib.fitmodel) grand() (egglib.egglib_binding.Random method) group (egglib.SequenceItem attribute) group() (egglib.Align method) (egglib.Container method) (egglib.egglib_binding.Align method) (egglib.egglib_binding.Container method) groupByName() (egglib.Align method) (egglib.Container method) groups() (egglib.Align method) (egglib.Container method) growthRate() (egglib.egglib_binding.ParamSet method) GrowthRateChange (class in egglib.egglib_binding) Gst() (egglib.egglib_binding.HaplotypeDiversity method)

H

H() (egglib.egglib_binding.BppDiversity method) (egglib.egglib_binding.NucleotideDiversity method) HaplotypeDiversity (class in egglib.egglib_binding) haplotypeIndex() (egglib.egglib_binding.HaplotypeDiversity method) hasOutgroup() (egglib.egglib_binding.BppDiversity method) hasSpecificAllele() (egglib.egglib_binding.SitePolymorphism method) haveCommonAllele() (egglib.egglib_binding.SitePolymorphism method) haveFixedDifference() (egglib.egglib_binding.SitePolymorphism method)

haveSharedAllele() (egglib.egglib_binding.SitePolymorphism method) He() (egglib.egglib_binding.BppDiversity method) (egglib.egglib_binding.HaplotypeDiversity method) (egglib.egglib_binding.MicrosatelliteDiversity method) He2() (egglib.egglib_binding.BppDiversity method) HFStatistics (class in egglib.egglib_binding) hslice() (egglib.egglib_binding.Align method) (egglib.egglib_binding.Container method) Hst() (egglib.egglib_binding.HaplotypeDiversity method)

I

IM (class in egglib.fitmodel) IMG (class in egglib.fitmodel) IMiG (class in egglib.fitmodel) IMiGn (class in egglib.fitmodel) IMn (class in egglib.fitmodel) import_posterior() (in module egglib.fitmodel) inconsistentPositions() (egglib.egglib_binding.Consensus method) increment() (egglib.tools.Updater method) index() (egglib.tools.GeneticCodes class method) irand() (egglib.egglib_binding.Random method)

is_ascendant() (egglib.TreeNode method) is_descendant() (egglib.TreeNode method) is_start() (egglib.tools.GeneticCodes class method) isComplement() (egglib.GenBankFeatureLocation method) isEqual() (egglib.Container method) (egglib.egglib_binding.Align method) (egglib.egglib_binding.Container method) isOrientable() (egglib.egglib_binding.SitePolymorphism method) isPolymorphic() (egglib.egglib_binding.SitePolymorphism method) isRange() (egglib.GenBankFeatureLocation method) iterator() (egglib.fitmodel.Dataset method)

J

JFS (class in egglib.fitmodel)

K

K() (egglib.egglib_binding.BppDiversity method) (egglib.egglib_binding.HaplotypeDiversity method)

Kst() (egglib.egglib_binding.HaplotypeDiversity method)

L

label() (egglib.egglib_binding.Edge method) last_node() (egglib.Tree method) lateralize() (egglib.Tree method) LD() (in module egglib.tools) leaves_down() (egglib.TreeNode method) leaves_up() (egglib.TreeNode method) length (egglib.egglib_binding.Edge attribute) LinkageDisequilibrium (class in egglib.egglib_binding)

load() (egglib.egglib_binding.BppDiversity method) (egglib.SSR method) (egglib.egglib_binding.HaplotypeDiversity method) (egglib.egglib_binding.LinkageDisequilibrium method) (egglib.egglib_binding.MicrosatelliteDiversity method) (egglib.egglib_binding.NucleotideDiversity method) (egglib.egglib_binding.SitePolymorphism method) loadIndividual() (egglib.egglib_binding.FStatistics method) (egglib.egglib_binding.HFStatistics method) locate() (in module egglib.tools) longest_orf() (in module egglib.tools) ls() (egglib.Align method) (egglib.Container method) (egglib.egglib_binding.Align method) (egglib.egglib_binding.Container method) lseff() (egglib.egglib_binding.NucleotideDiversity method) lseffo() (egglib.egglib_binding.NucleotideDiversity method)

M

Mase (class in egglib.tools) matches() (egglib.Align method) (egglib.Container method) matrixLD() (egglib.Align method) MicrosatelliteDiversity (class in egglib.egglib_binding) midroot() (egglib.Tree method) migrationRate() (egglib.egglib_binding.ParamSet method) MK() (egglib.egglib_binding.BppDiversity method) models (in module egglib.fitmodel) mother() (egglib.egglib_binding.PopulationFusion method) motifs() (in module egglib.tools) moveAllLineages() (egglib.egglib_binding.Controller method)

moveSomeLineages() (egglib.egglib_binding.Controller method) MRC (class in egglib.fitmodel) MRCA() (egglib.egglib_binding.Arg method) Ms (class in egglib.egglib_binding) ms() (in module egglib.wrappers) muscle() (in module egglib.wrappers) mutationModel() (egglib.egglib_binding.Mutator method) mutationRate() (egglib.egglib_binding.Mutator method) Mutator (class in egglib.egglib_binding) mute() (egglib.egglib_binding.Arg method) (egglib.egglib_binding.Mutator method)

N

name (egglib.SequenceItem attribute) name() (egglib.Align method) (egglib.Container method) (egglib.egglib_binding.Align method) (egglib.egglib_binding.Container method) names() (egglib.Align method) (egglib.Container method) ncodon1mut() (egglib.egglib_binding.BppDiversity method) newick() (egglib.egglib_binding.Arg method) (egglib.Tree method) nextChangeDate() (egglib.egglib_binding.ParamSet method) nextChangeDo() (egglib.egglib_binding.ParamSet method) nexus() (egglib.Align method) NI() (egglib.egglib_binding.BppDiversity method) nj() (in module egglib.wrappers) no_duplicates() (egglib.Align method) (egglib.Container method) npop() (egglib.egglib_binding.NucleotideDiversity method) nrand() (egglib.egglib_binding.Random method) ns() (egglib.Align method) (egglib.Container method) (egglib.egglib_binding.Align method) (egglib.egglib_binding.Container method) (egglib.egglib_binding.SitePolymorphism method) nseff() (egglib.egglib_binding.NucleotideDiversity method) nseffo() (egglib.egglib_binding.NucleotideDiversity method) NSsites() (egglib.egglib_binding.BppDiversity method) nstop() (egglib.egglib_binding.BppDiversity method) nsyn() (egglib.egglib_binding.BppDiversity method) NucleotideDiversity (class in egglib.egglib_binding) number_of_categories() (egglib.wrappers.Codeml method) number_of_features() (egglib.GenBank method) number_of_leaves() (egglib.Tree method)

number_of_nodes() (egglib.Tree method) number_of_params() (egglib.fitmodel.PriorDiscrete method) (egglib.fitmodel.PriorDumb method) number_of_samples() (egglib.egglib_binding.ABC method) number_of_statistics() (egglib.egglib_binding.ABC method) numberOfAlleles() (egglib.egglib_binding.FStatistics method) (egglib.egglib_binding.HFStatistics method) (egglib.egglib_binding.MicrosatelliteDiversity method) (egglib.egglib_binding.Mutator method) (egglib.egglib_binding.SitePolymorphism method) numberOfAscendants() (egglib.TreeNode method) numberOfDescendants() (egglib.TreeNode method) numberOfEdges (egglib.egglib_binding.Arg attribute) numberOfGenotypes() (egglib.egglib_binding.FStatistics method) (egglib.SSR method) (egglib.egglib_binding.HFStatistics method) numberOfLoci() (egglib.SSR method) numberOfMutations() (egglib.egglib_binding.Mutator method) (egglib.simul.CoalesceFiniteAlleleMutator method) (egglib.simul.CoalesceInfiniteAlleleMutator method) (egglib.simul.CoalesceMutator method) (egglib.simul.CoalesceStepwiseMutator method) (egglib.simul.CoalesceTwoPhaseMutator method) numberOfPairs() (egglib.egglib_binding.LinkageDisequilibrium method) numberOfPopulations() (egglib.egglib_binding.Current method) (egglib.egglib_binding.FStatistics method) (egglib.egglib_binding.HFStatistics method) (egglib.egglib_binding.ParamSet method) (egglib.egglib_binding.SitePolymorphism method) numberOfRecombinationEvents (egglib.egglib_binding.Arg attribute) numberOfRelatives() (egglib.TreeNode method) numberOfSamples (egglib.egglib_binding.Arg attribute) numberOfSamples() (egglib.egglib_binding.ParamSet method) numberOfSegments (egglib.egglib_binding.Arg attribute) numberOfSegments() (egglib.egglib_binding.ParamSet method) numberOfSequences() (egglib.egglib_binding.Align method) (egglib.egglib_binding.CharMatrix method) (egglib.egglib_binding.DataMatrix method) numberOfSites() (egglib.egglib_binding.Align method) (egglib.egglib_binding.CharMatrix method) (egglib.egglib_binding.DataMatrix method) (egglib.egglib_binding.MicrosatelliteDiversity method) (egglib.egglib_binding.Mutator method) numberOfSons (egglib.egglib_binding.Edge attribute)

O

obs() (egglib.egglib_binding.ABC method) Option (class in egglib.utils)

options (egglib.utils.BaseCommand attribute) outgroup() (egglib.egglib_binding.SitePolymorphism method)

P

pairs() (egglib.wrappers.Primer3 method) pairwiseMigrationRate() (egglib.egglib_binding.ParamSet method) ParamSample (class in egglib.fitmodel) ParamSet (class in egglib.egglib_binding) parse() (egglib.egglib_binding.Fasta static method) (egglib.GenBankFeature method) (egglib.SSR method) (egglib.egglib_binding.Staden static method) (egglib.fitmodel.PriorDiscrete method) (egglib.fitmodel.PriorDumb method) parsef() (egglib.egglib_binding.Fasta static method) path() (egglib.wrappers.BLASTdb method) PEM (class in egglib.fitmodel) phylip() (egglib.Align method) phyml() (egglib.Align method) (in module egglib.wrappers) Pi() (egglib.egglib_binding.NucleotideDiversity method) PiNS() (egglib.egglib_binding.BppDiversity method) PiS() (egglib.egglib_binding.BppDiversity method) polymorphic_positions() (egglib.egglib_binding.NucleotideDiversity method) polymorphism() (egglib.Align method) polymorphismBPP() (egglib.Align method) Polymorphisms() (egglib.egglib_binding.NucleotideDiversity method) pop_Pi() (egglib.egglib_binding.NucleotideDiversity method) popLabel() (egglib.egglib_binding.NucleotideDiversity method) pops() (egglib.fitmodel.Dataset method) population() (egglib.egglib_binding.Current method) (egglib.egglib_binding.PopulationBottleneck method) (egglib.egglib_binding.PopulationGrowthRateChange method) (egglib.egglib_binding.PopulationParamChange method) (egglib.egglib_binding.PopulationSplit method) (egglib.egglib_binding.SinglePopulationSizeChange method)

PopulationBottleneck (class in egglib.egglib_binding) populationFrequency() (egglib.egglib_binding.FStatistics method) (egglib.egglib_binding.HFStatistics method) PopulationFusion (class in egglib.egglib_binding) populationFusion() (egglib.simul.CoalesceParamSet method) PopulationGrowthRateChange (class in egglib.egglib_binding) populationLabel() (egglib.egglib_binding.Align method) (egglib.egglib_binding.CharMatrix method) (egglib.egglib_binding.DataMatrix method) (egglib.egglib_binding.FStatistics method) (egglib.egglib_binding.HFStatistics method) populationNumberOfLineages() (egglib.egglib_binding.Current method) PopulationParamChange (class in egglib.egglib_binding) populationSize() (egglib.egglib_binding.ParamSet method) PopulationSplit (class in egglib.egglib_binding) populationSplit() (egglib.simul.CoalesceParamSet method) prand() (egglib.egglib_binding.Random method) Primer3 (class in egglib.wrappers) PriorDiscrete (class in egglib.fitmodel) PriorDumb (class in egglib.fitmodel) PriorParseError (class in egglib.fitmodel) priors (in module egglib.fitmodel) prob() (egglib.egglib_binding.Ms static method) probability() (egglib.egglib_binding.PopulationSplit method) process_cmdline_arguments() (egglib.utils.BaseCommand method)

Q

qualifiers() (egglib.GenBankFeature method)

quiet (egglib.utils.BaseCommand attribute)

R

r() (egglib.egglib_binding.LinkageDisequilibrium method) r2() (egglib.egglib_binding.LinkageDisequilibrium method) Random (class in egglib.egglib_binding) randomAncestralAllele() (egglib.egglib_binding.Mutator method) ranges() (in module egglib.tools) rc() (egglib.GenBank method) (egglib.GenBankFeature method) (egglib.GenBankFeatureLocation method) (in module egglib.tools) ReadingFrame (class in egglib.tools) recombination() (egglib.egglib_binding.Arg method) (egglib.egglib_binding.Edge method) recombinationRate() (egglib.egglib_binding.ParamSet method) refresh() (egglib.tools.Updater method) regression() (egglib.egglib_binding.ABC method) rejection() (egglib.egglib_binding.ABC method) remove() (egglib.Align method) (egglib.Container method) (egglib.egglib_binding.Align method) (egglib.egglib_binding.Container method) remove_ascendant() (egglib.TreeNode method) remove_descendant() (egglib.TreeNode method)

remove_node() (egglib.Tree method) removePosition() (egglib.Align method) (egglib.egglib_binding.Align method) rename() (egglib.Align method) (egglib.Container method) reoriente() (egglib.Tree method) reserve() (egglib.egglib_binding.BaseDiversity method) (egglib.egglib_binding.FStatistics method) (egglib.egglib_binding.HFStatistics method) (egglib.egglib_binding.HaplotypeDiversity method) (egglib.egglib_binding.LinkageDisequilibrium method) (egglib.egglib_binding.NucleotideDiversity method) reset() (egglib.egglib_binding.Arg method) (egglib.egglib_binding.BaseDiversity method) (egglib.egglib_binding.Controller method) (egglib.egglib_binding.Current method) (egglib.egglib_binding.Edge method) (egglib.egglib_binding.HaplotypeDiversity method) (egglib.egglib_binding.LinkageDisequilibrium method) (egglib.egglib_binding.Mutator method) (egglib.egglib_binding.NucleotideDiversity method) (egglib.egglib_binding.ParamSet method) resize() (egglib.egglib_binding.DataMatrix method) reverse() (egglib.TreeNode method) reverse_primers() (egglib.wrappers.Primer3 method) rhoH() (egglib.egglib_binding.BppDiversity method) Rmin() (egglib.Align method) (egglib.egglib_binding.LinkageDisequilibrium method) root() (egglib.Tree method) root_node() (egglib.Tree method) roots() (egglib.egglib_binding.Consensus method) run() (egglib.utils.BaseCommand method)

S

S() (egglib.egglib_binding.BppDiversity method) (egglib.egglib_binding.NucleotideDiversity method) samples() (egglib.simul.CoalesceParamSet method) sd() (egglib.egglib_binding.ABC method) secondSequenceNames() (egglib.egglib_binding.Consensus method) seed1() (egglib.egglib_binding.Random method) seed2() (egglib.egglib_binding.Random method) segment() (egglib.egglib_binding.Edge method) segmentLengths (egglib.egglib_binding.Arg attribute) select() (egglib.wrappers.Primer3 method) selfingRate() (egglib.egglib_binding.ParamSet method) SelfingRateChange (class in egglib.egglib_binding) sequence (egglib.SequenceItem attribute) sequence() (egglib.Align method) (egglib.Container method) (egglib.egglib_binding.Align method) (egglib.egglib_binding.Container method) sequenceByName() (egglib.Align method) (egglib.Container method) SequenceItem (class in egglib) set() (egglib.Align method) (egglib.Container method) (egglib.GenBankFeature method) (egglib.egglib_binding.Align method) (egglib.egglib_binding.Arg method) (egglib.egglib_binding.Container method) (egglib.egglib_binding.DataMatrix method) set_branch_from() (egglib.TreeNode method) set_branch_to() (egglib.TreeNode method) set_label() (egglib.TreeNode method) set_sequence() (egglib.GenBank method) set_terminal() (egglib.egglib_binding.Edge method) setComplement() (egglib.GenBankFeatureLocation method) setDisagreement() (egglib.egglib_binding.Consensus method) setGroups() (egglib.egglib_binding.ParamSet method) setMissing() (egglib.egglib_binding.Consensus method) setNotComplement() (egglib.GenBankFeatureLocation method) setSites() (egglib.simul.CoalesceFiniteAlleleMutator method) (egglib.simul.CoalesceInfiniteAlleleMutator method) (egglib.simul.CoalesceMutator method) (egglib.simul.CoalesceStepwiseMutator method) (egglib.simul.CoalesceTwoPhaseMutator method) Sext() (egglib.egglib_binding.BppDiversity method) SFS (class in egglib.fitmodel) SharedAlleles() (egglib.egglib_binding.NucleotideDiversity method) shift() (egglib.egglib_binding.DataMatrix method) (egglib.GenBankFeature method) (egglib.GenBankFeatureLocation method) shuffle() (egglib.Align method) (egglib.Container method) simErrors() (egglib.Align method) Sinf() (egglib.egglib_binding.BppDiversity method) SingleMigrationRateChange (class in egglib.egglib_binding) SingleParamChange (class in egglib.egglib_binding) singlePopulationBottleneck() (egglib.simul.CoalesceParamSet method) SinglePopulationSizeChange (class in egglib.egglib_binding)

singles() (egglib.egglib_binding.ParamSet method) singleton_positions() (egglib.egglib_binding.NucleotideDiversity method) site1() (egglib.egglib_binding.LinkageDisequilibrium method) site2() (egglib.egglib_binding.LinkageDisequilibrium method) SitePolymorphism (class in egglib.egglib_binding) sitePosition() (egglib.egglib_binding.Align method) (egglib.egglib_binding.CharMatrix method) (egglib.egglib_binding.DataMatrix method) (egglib.egglib_binding.Mutator method) siteWeight() (egglib.egglib_binding.Mutator method) sizeVariance() (egglib.egglib_binding.MicrosatelliteDiversity method) slice() (egglib.Align method) (egglib.Container method) slider() (egglib.Align method) SM (class in egglib.fitmodel) smallest_group() (egglib.Tree method) smallest_monophyleticGroup() (egglib.Tree method) SNM (class in egglib.fitmodel) Snn() (egglib.egglib_binding.HaplotypeDiversity method) SNS() (egglib.egglib_binding.BppDiversity method) So() (egglib.egglib_binding.NucleotideDiversity method) son1 (egglib.egglib_binding.Edge attribute) son2 (egglib.egglib_binding.Edge attribute) sort() (egglib.TreeNode method) (egglib.wrappers.Primer3 method) sort_aligns() (egglib.fitmodel.Dataset method) source() (egglib.egglib_binding.SingleMigrationRateChange method) SpecificAlleles() (egglib.egglib_binding.NucleotideDiversity method) SpecificDerivedAlleles() (egglib.egglib_binding.NucleotideDiversity method) SS() (egglib.egglib_binding.BppDiversity method) Ssin() (egglib.egglib_binding.BppDiversity method) Ssites() (egglib.egglib_binding.BppDiversity method) SSR (class in egglib) Staden (class in egglib.egglib_binding) staden() (in module egglib.tools) start() (egglib.GenBankFeature method) start_omega() (egglib.wrappers.Codeml method) stats() (egglib.SSR method) (egglib.tools.Updater method) step() (egglib.egglib_binding.Controller method) stop() (egglib.GenBankFeature method) str() (egglib.Align method) (egglib.Container method) (egglib.SSR method) (egglib.TreeNode method) (egglib.fitmodel.PriorDiscrete method) (egglib.fitmodel.PriorDumb method) summstats (in module egglib.fitmodel)

T

T1() (egglib.egglib_binding.HFStatistics method) T2() (egglib.egglib_binding.HFStatistics method) T83() (egglib.egglib_binding.BppDiversity method) tblastn() (egglib.wrappers.BL2SEQ method) (egglib.wrappers.BLAST method) tblastx() (egglib.wrappers.BL2SEQ method) (egglib.wrappers.BLAST method) test_all() (in module egglib.test) theta() (egglib.egglib_binding.FStatistics method) (egglib.egglib_binding.HFStatistics method) thetaAssumingIAM() (egglib.egglib_binding.MicrosatelliteDiversity method) thetaAssumingSMMfromHe() (egglib.egglib_binding.MicrosatelliteDiversity method) thetaAssumingSMMfromSizeVariance() (egglib.egglib_binding.MicrosatelliteDiversity method) thetaH() (egglib.egglib_binding.NucleotideDiversity method) thetaL() (egglib.egglib_binding.NucleotideDiversity method) thetaW() (egglib.egglib_binding.NucleotideDiversity method) threshold() (egglib.egglib_binding.ABC method) Ti() (egglib.egglib_binding.BppDiversity method) TIGR (class in egglib) time() (egglib.egglib_binding.Arg method) TiTv() (egglib.egglib_binding.BppDiversity method) tMRCA() (egglib.egglib_binding.Ms static method) top (egglib.egglib_binding.Edge attribute)

total_length() (egglib.Tree method) totalLength (egglib.egglib_binding.Arg attribute) totalNumberOfLineages() (egglib.egglib_binding.Current method) TPH (class in egglib.fitmodel) TPMparam() (egglib.egglib_binding.Mutator method) TPMproba() (egglib.egglib_binding.Mutator method) TPS (class in egglib.fitmodel) transitionWeight() (egglib.egglib_binding.Mutator method) transitionWeights() (egglib.simul.CoalesceFiniteAlleleMutator method) translate() (egglib.tools.GeneticCodes class method) (in module egglib.tools) Tree (class in egglib) TreeNode (class in egglib) trees() (egglib.egglib_binding.Ms static method) triConfiguration() (egglib.egglib_binding.NucleotideDiversity method) Tv() (egglib.egglib_binding.BppDiversity method) tW() (egglib.egglib_binding.BppDiversity method) tWNS() (egglib.egglib_binding.BppDiversity method) tWS() (egglib.egglib_binding.BppDiversity method) type() (egglib.GenBankFeature method)

U

unfix_omega() (egglib.wrappers.Codeml method) ungap() (in module egglib.tools) uniform() (egglib.egglib_binding.Random method)

uninformativePositions() (egglib.egglib_binding.Consensus method) unlink() (egglib.TreeNode method) Updater (class in egglib.tools)

V

Vallele() (egglib.egglib_binding.FStatistics method) value() (egglib.egglib_binding.AllMigrationRateChange method) (egglib.egglib_binding.AllPopulationSizeChange method) (egglib.egglib_binding.Bottleneck method) (egglib.egglib_binding.GrowthRateChange method) (egglib.egglib_binding.PopulationBottleneck method) (egglib.egglib_binding.PopulationGrowthRateChange method) (egglib.egglib_binding.PopulationParamChange method) (egglib.egglib_binding.SelfingRateChange method) (egglib.egglib_binding.SingleMigrationRateChange method) (egglib.egglib_binding.SingleParamChange method) (egglib.egglib_binding.SinglePopulationSizeChange method) values() (egglib.fitmodel.ParamSample method)

Vindividual() (egglib.egglib_binding.FStatistics method) Vpopulation() (egglib.egglib_binding.FStatistics method) vslice() (egglib.egglib_binding.Align method)

W

wipe() (egglib.tools.Updater method) wrap() (in module egglib.tools)

write() (egglib.Align method) (egglib.Container method) (egglib.GenBank method) (egglib.Tree method) write_stream() (egglib.GenBank method)

Z

Z() (egglib.egglib_binding.NucleotideDiversity method)