EggLib

Index

A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W

A

AA (egglib.io.Variant attribute)
AC (egglib.io.Variant attribute)
add() (egglib.coalesce.EventList method)
add_base_choice() (egglib.io.GenBankFeatureLocation method)
add_base_range() (egglib.io.GenBankFeatureLocation method)
add_between_base() (egglib.io.GenBankFeatureLocation method)
add_event() (egglib.coalesce.ParamDict method)
add_feature() (egglib.io.GenBank method)
add_node() (egglib.Tree method)
add_outgroup() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
add_qualifier() (egglib.io.GenBankFeature method)
add_sample() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
add_samples() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
add_single_base() (egglib.io.GenBankFeatureLocation method)
add_stats() (egglib.stats.ComputeStats method)
AF (egglib.io.Variant attribute)
aliases (egglib.io.GFF3Feature attribute)
Align (class in egglib)
align (egglib.coalesce.Simulator attribute)
alignment (egglib.tools.BackalignError attribute)
all_stats() (egglib.stats.ComputeStats method)
alleles (egglib.io.Variant attribute)
alleles() (egglib.stats.Site method)
alt_type_breakend (egglib.io.Variant attribute)
alt_type_default (egglib.io.Variant attribute)
alt_type_referred (egglib.io.Variant attribute)
alternate_types (egglib.io.Variant attribute)
AN (egglib.io.Variant attribute)
as_dict() (egglib.stats.Structure method)
as_list() (egglib.stats.Site method)
as_order() (egglib.io.GenBankFeatureLocation method)
as_range() (egglib.io.GenBankFeatureLocation method)
attributes (egglib.io.GFF3Feature attribute)
autodetect() (egglib.wrappers.paths method)

B

backalign() (in module egglib.tools)
BackalignError (class in egglib.tools)
base (egglib.Tree attribute)
bed_slider() (egglib.io.VcfParser method)
BEFORE (C++ member)
bernoulli() (egglib.tools.Random method)
binomial() (egglib.tools.Random method)
boolean() (egglib.tools.Random method)
bounds (egglib.tools.Discretize attribute)
branch_to() (egglib.Node method)
breadth_iter() (egglib.Tree method)

C

child() (egglib.Node method)
children() (egglib.Node method)
chromosome (egglib.io._vcf.VcfWindow attribute)
(egglib.io.Variant attribute)
clean() (egglib.misc.TempFile method)
clean_branch_lengths() (egglib.Tree method)
clean_internal_labels() (egglib.Tree method)
clear() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
(egglib.coalesce.EventList method)
clear_stats() (egglib.stats.ComputeStats method)
clustal() (in module egglib.wrappers)
codeml() (in module egglib.wrappers)
CodingDiversity (class in egglib.stats)
codon_bases() (egglib.tools.ReadingFrame method)
codon_index() (egglib.tools.ReadingFrame method)
codon_position() (egglib.tools.ReadingFrame method)
collapse() (egglib.Tree method)
column() (egglib.Align method)
compare() (in module egglib.tools)
compute() (egglib.stats.ProbaMisoriented method)
ComputeStats (class in egglib.stats)
concat() (in module egglib.tools)
configuration() (egglib.io._vcf.VcfWindow method)
configure() (egglib.io._vcf.VcfWindow method)
(egglib.stats.ComputeStats method)
consensus() (egglib.Align method)
Container (class in egglib)
copy() (egglib.coalesce.ParamDict method)
(egglib.Tree method)
(egglib.io.GenBankFeature method)
(egglib.io.GenBankFeatureLocation method)
count() (egglib.coalesce.ParamList method)
(egglib.coalesce.ParamMatrix method)
create() (egglib._interface.DataBase class method)
(egglib.Align class method)
(egglib.Container class method)
cur_haplotypes (egglib.stats.EHH attribute)

D

D (egglib.stats.ProbaMisoriented attribute)
DataBase (class in egglib._interface)
dbxref (egglib.io.GFF3Feature attribute)
del_columns() (egglib.Align method)
del_outgroup() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
del_sample() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
del_sites() (egglib.Container method)
del_sites_o() (egglib.Container method)
delete_truncated (egglib.tools.Translator attribute)
depth_iter() (egglib.Tree method)
derives_from (egglib.io.GFF3Feature attribute)
disable_trans_matrix() (egglib.coalesce.ParamDict method)
Discretize (class in egglib.tools)
done_EHH() (egglib.stats.EHH method)
done_EHHc() (egglib.stats.EHH method)

E

egglib.stats.multiallelic_ignore (built-in variable)
egglib.stats.multiallelic_use_all (built-in variable)
egglib.stats.multiallelic_use_main (built-in variable)
egglib.tools.ungap() (built-in function)
egglib::ABC (C++ class)
egglib::ABC::ABC (C++ function)
egglib::ABC::add_fname (C++ function)
egglib::ABC::get_threshold (C++ function)
egglib::ABC::LOG (C++ class)
egglib::ABC::NONE (C++ class)
egglib::ABC::number_of_samples (C++ function)
egglib::ABC::number_of_samples_part (C++ function)
egglib::ABC::number_of_statistics (C++ function)
egglib::ABC::obs (C++ function)
egglib::ABC::regression (C++ function)
egglib::ABC::rejection (C++ function)
egglib::ABC::sd (C++ function)
egglib::ABC::TAN (C++ class)
egglib::ABC::threshold (C++ function)
egglib::ABC::TransformMode (C++ type)
egglib::ABC::~ABC (C++ function)
egglib::AlleleStatus (C++ class)
egglib::AlleleStatus::AlleleStatus (C++ function)
egglib::AlleleStatus::FxA (C++ function)
egglib::AlleleStatus::FxA_T1 (C++ function)
egglib::AlleleStatus::FxD (C++ function)
egglib::AlleleStatus::FxD_T1 (C++ function)
egglib::AlleleStatus::nsites (C++ function)
egglib::AlleleStatus::nsites_o (C++ function)
egglib::AlleleStatus::process (C++ function)
egglib::AlleleStatus::reset (C++ function)
egglib::AlleleStatus::ShA (C++ function)
egglib::AlleleStatus::ShA_T1 (C++ function)
egglib::AlleleStatus::ShP (C++ function)
egglib::AlleleStatus::ShP_T1 (C++ function)
egglib::AlleleStatus::Sp (C++ function)
egglib::AlleleStatus::Sp_T1 (C++ function)
egglib::AlleleStatus::Spd (C++ function)
egglib::AlleleStatus::Spd_T1 (C++ function)
egglib::AlleleStatus::total (C++ function)
egglib::AlleleStatus::~AlleleStatus (C++ function)
egglib::BaseFormatter (C++ class)
egglib::BaseFormatter::BaseFormatter (C++ function)
egglib::BaseFormatter::close (C++ function)
egglib::BaseFormatter::flush (C++ function)
egglib::BaseFormatter::get_str (C++ function)
egglib::BaseFormatter::open_file (C++ function)
egglib::BaseFormatter::to_cout (C++ function)
egglib::BaseFormatter::to_str (C++ function)
egglib::BaseFormatter::write (C++ function)
egglib::BaseFormatter::~BaseFormatter (C++ function)
egglib::Coalesce (C++ class)
egglib::Coalesce::admixt (C++ function)
egglib::Coalesce::bottleneck (C++ function)
egglib::Coalesce::Coalesce (C++ function)
egglib::Coalesce::coalescence (C++ function)
egglib::Coalesce::data (C++ function)
egglib::Coalesce::delayedSample (C++ function)
egglib::Coalesce::migrate (C++ function)
egglib::Coalesce::mutate (C++ function)
egglib::Coalesce::number_of_trees (C++ function)
egglib::Coalesce::simul (C++ function)
egglib::Coalesce::site_position (C++ function)
egglib::Coalesce::tree (C++ function)
egglib::Coalesce::tree_start (C++ function)
egglib::Coalesce::tree_stop (C++ function)
egglib::Coalesce::~Coalesce (C++ function)
egglib::CodingSite (C++ class)
egglib::CodingSite::aminoacids (C++ function)
egglib::CodingSite::CodingSite (C++ function)
egglib::CodingSite::codons (C++ function)
egglib::CodingSite::mutated (C++ function)
egglib::CodingSite::ndiff (C++ function)
egglib::CodingSite::ni (C++ function)
egglib::CodingSite::no (C++ function)
egglib::CodingSite::NS (C++ function)
egglib::CodingSite::nseff (C++ function)
egglib::CodingSite::nseffo (C++ function)
egglib::CodingSite::NSsites (C++ function)
egglib::CodingSite::nstop (C++ function)
egglib::CodingSite::pl (C++ function)
egglib::CodingSite::process (C++ function)
egglib::CodingSite::Ssites (C++ function)
egglib::CodingSite::~CodingSite (C++ function)
egglib::ComputeV (C++ class)
egglib::ComputeV::average (C++ function)
egglib::ComputeV::compute (C++ function)
egglib::ComputeV::ComputeV (C++ function)
egglib::ComputeV::num_sites (C++ function)
egglib::ComputeV::reset (C++ function)
egglib::ComputeV::set_allele (C++ function)
egglib::ComputeV::setup_alleles (C++ function)
egglib::ComputeV::setup_alleles_from_site (C++ function)
egglib::ComputeV::~ComputeV (C++ function)
egglib::DataHolder (C++ class)
egglib::DataHolder::clear (C++ function)
egglib::DataHolder::DataHolder (C++ function), [1]
egglib::DataHolder::del_sample_i (C++ function)
egglib::DataHolder::del_sample_o (C++ function)
egglib::DataHolder::del_sites (C++ function)
egglib::DataHolder::del_sites_i (C++ function)
egglib::DataHolder::del_sites_o (C++ function)
egglib::DataHolder::find (C++ function)
egglib::DataHolder::get_group_i (C++ function)
egglib::DataHolder::get_group_o (C++ function)
egglib::DataHolder::get_i (C++ function)
egglib::DataHolder::get_is_matrix (C++ function)
egglib::DataHolder::get_name_i (C++ function)
egglib::DataHolder::get_name_o (C++ function)
egglib::DataHolder::get_ngroups (C++ function)
egglib::DataHolder::get_nsam_i (C++ function)
egglib::DataHolder::get_nsam_o (C++ function)
egglib::DataHolder::get_nsit (C++ function)
egglib::DataHolder::get_nsit_i (C++ function)
egglib::DataHolder::get_nsit_o (C++ function)
egglib::DataHolder::get_o (C++ function)
egglib::DataHolder::insert_sites (C++ function)
egglib::DataHolder::insert_sites_i (C++ function)
egglib::DataHolder::insert_sites_o (C++ function)
egglib::DataHolder::is_equal (C++ function)
egglib::DataHolder::name_append_i (C++ function)
egglib::DataHolder::name_append_o (C++ function)
egglib::DataHolder::name_appendch_i (C++ function)
egglib::DataHolder::name_appendch_o (C++ function)
egglib::DataHolder::operator= (C++ function)
egglib::DataHolder::reserve (C++ function)
egglib::DataHolder::reset (C++ function)
egglib::DataHolder::set_group_i (C++ function)
egglib::DataHolder::set_group_o (C++ function)
egglib::DataHolder::set_i (C++ function)
egglib::DataHolder::set_is_matrix (C++ function)
egglib::DataHolder::set_name_i (C++ function)
egglib::DataHolder::set_name_o (C++ function)
egglib::DataHolder::set_ngroups (C++ function)
egglib::DataHolder::set_nsam_i (C++ function)
egglib::DataHolder::set_nsam_o (C++ function)
egglib::DataHolder::set_nsit (C++ function)
egglib::DataHolder::set_nsit_i (C++ function)
egglib::DataHolder::set_nsit_o (C++ function)
egglib::DataHolder::set_o (C++ function)
egglib::DataHolder::to_outgroup (C++ function)
egglib::DataHolder::valid_phyml_aa (C++ function)
egglib::DataHolder::valid_phyml_names (C++ function)
egglib::DataHolder::valid_phyml_nt (C++ function)
egglib::DataHolder::~DataHolder (C++ function)
egglib::Diversity1 (C++ class)
egglib::Diversity1::compute (C++ function)
egglib::Diversity1::D (C++ function)
egglib::Diversity1::Da (C++ function)
egglib::Diversity1::Deta (C++ function)
egglib::Diversity1::Dfl (C++ function)
egglib::Diversity1::Diversity1 (C++ function)
egglib::Diversity1::Dstar (C++ function)
egglib::Diversity1::Dxy (C++ function)
egglib::Diversity1::E (C++ function)
egglib::Diversity1::eta (C++ function)
egglib::Diversity1::etao (C++ function)
egglib::Diversity1::F (C++ function)
egglib::Diversity1::Fstar (C++ function)
egglib::Diversity1::Hns (C++ function)
egglib::Diversity1::Hsd (C++ function)
egglib::Diversity1::load (C++ function)
egglib::Diversity1::ls (C++ function)
egglib::Diversity1::lso (C++ function)
egglib::Diversity1::lt (C++ function)
egglib::Diversity1::nM (C++ function)
egglib::Diversity1::ns_set (C++ function)
egglib::Diversity1::nseff (C++ function)
egglib::Diversity1::nseffo (C++ function)
egglib::Diversity1::nsingld (C++ function)
egglib::Diversity1::nsmax (C++ function)
egglib::Diversity1::nsmaxo (C++ function)
egglib::Diversity1::Pi (C++ function)
egglib::Diversity1::pM (C++ function)
egglib::Diversity1::reset (C++ function)
egglib::Diversity1::S (C++ function)
egglib::Diversity1::set_option_multiple (C++ function)
egglib::Diversity1::singl (C++ function)
egglib::Diversity1::singl_o (C++ function)
egglib::Diversity1::site (C++ function)
egglib::Diversity1::site_o (C++ function)
egglib::Diversity1::So (C++ function)
egglib::Diversity1::Ss (C++ function)
egglib::Diversity1::Sso (C++ function)
egglib::Diversity1::thetaH (C++ function)
egglib::Diversity1::thetaL (C++ function)
egglib::Diversity1::thetaPi (C++ function)
egglib::Diversity1::thetaW (C++ function)
egglib::Diversity1::toggle_basic (C++ function)
egglib::Diversity1::toggle_off (C++ function)
egglib::Diversity1::toggle_ori_div (C++ function)
egglib::Diversity1::toggle_ori_site (C++ function)
egglib::Diversity1::toggle_site_lists (C++ function)
egglib::Diversity1::~Diversity1 (C++ function)
egglib::Diversity2 (C++ class)
egglib::Diversity2::B (C++ function)
egglib::Diversity2::Ch (C++ function)
egglib::Diversity2::ChE (C++ function)
egglib::Diversity2::compute (C++ function)
egglib::Diversity2::Diversity2 (C++ function)
egglib::Diversity2::k (C++ function)
egglib::Diversity2::ko (C++ function)
egglib::Diversity2::load (C++ function)
egglib::Diversity2::num_clear (C++ function)
egglib::Diversity2::num_orientable (C++ function)
egglib::Diversity2::num_sequences (C++ function)
egglib::Diversity2::num_sites (C++ function)
egglib::Diversity2::Q (C++ function)
egglib::Diversity2::R2 (C++ function)
egglib::Diversity2::R2E (C++ function)
egglib::Diversity2::R3 (C++ function)
egglib::Diversity2::R3E (C++ function)
egglib::Diversity2::R4 (C++ function)
egglib::Diversity2::R4E (C++ function)
egglib::Diversity2::reset (C++ function)
egglib::Diversity2::set_option_multiple (C++ function)
egglib::Diversity2::toggle_off (C++ function)
egglib::Diversity2::toggle_partitions (C++ function)
egglib::Diversity2::toggle_singletons (C++ function)
egglib::Diversity2::~Diversity2 (C++ function)
egglib::EggArgumentValueError (C++ class)
egglib::EggArgumentValueError::EggArgumentValueError (C++ function)
egglib::EggArgumentValueError::~EggArgumentValueError (C++ function)
egglib::EggException (C++ class)
egglib::EggException::EggException (C++ function), [1]
egglib::EggException::what (C++ function)
egglib::EggException::~EggException (C++ function)
egglib::EggFormatError (C++ class)
egglib::EggFormatError::character (C++ function)
egglib::EggFormatError::EggFormatError (C++ function)
egglib::EggFormatError::info (C++ function)
egglib::EggFormatError::line (C++ function)
egglib::EggFormatError::m (C++ function)
egglib::EggFormatError::~EggFormatError (C++ function)
egglib::EggInvalidAlleleError (C++ class)
egglib::EggInvalidAlleleError::EggInvalidAlleleError (C++ function)
egglib::EggInvalidAlleleError::~EggInvalidAlleleError (C++ function)
egglib::EggMemoryError (C++ class)
egglib::EggMemoryError::EggMemoryError (C++ function)
egglib::EggMemoryError::~EggMemoryError (C++ function)
egglib::EggOpenFileError (C++ class)
egglib::EggOpenFileError::EggOpenFileError (C++ function)
egglib::EggOpenFileError::~EggOpenFileError (C++ function)
egglib::EggPloidyError (C++ class)
egglib::EggPloidyError::EggPloidyError (C++ function)
egglib::EggPloidyError::~EggPloidyError (C++ function)
egglib::EggRuntimeError (C++ class)
egglib::EggRuntimeError::EggRuntimeError (C++ function)
egglib::EggRuntimeError::~EggRuntimeError (C++ function)
egglib::EggUnalignedError (C++ class)
egglib::EggUnalignedError::EggUnalignedError (C++ function)
egglib::EggUnalignedError::~EggUnalignedError (C++ function)
egglib::EHH (C++ class)
egglib::EHH::dEHH (C++ function)
egglib::EHH::dEHH_max (C++ function)
egglib::EHH::dEHH_mean (C++ function)
egglib::EHH::dEHHc (C++ function)
egglib::EHH::dEHHG (C++ function)
egglib::EHH::dEHHS (C++ function)
egglib::EHH::EHH (C++ function)
egglib::EHH::EHHc (C++ function)
egglib::EHH::EHHG (C++ function)
egglib::EHH::EHHi (C++ function)
egglib::EHH::EHHS (C++ function)
egglib::EHH::flag_EHHG_done (C++ function)
egglib::EHH::flag_EHHS_done (C++ function)
egglib::EHH::iEG (C++ function)
egglib::EHH::iES (C++ function)
egglib::EHH::IHH (C++ function)
egglib::EHH::IHHc (C++ function)
egglib::EHH::iHS (C++ function)
egglib::EHH::K_core (C++ function)
egglib::EHH::K_cur (C++ function)
egglib::EHH::load_distant (C++ function)
egglib::EHH::num_avail_core (C++ function)
egglib::EHH::num_avail_cur (C++ function)
egglib::EHH::num_avail_tot (C++ function)
egglib::EHH::num_EHH_done (C++ function)
egglib::EHH::num_EHHc_done (C++ function)
egglib::EHH::rEHH (C++ function)
egglib::EHH::set_core (C++ function)
egglib::EHH::~EHH (C++ function)
egglib::Event (C++ class)
egglib::Event::admixture (C++ class)
egglib::Event::bottleneck (C++ class)
egglib::Event::change_G (C++ class)
egglib::Event::change_M (C++ class)
egglib::Event::change_Mp (C++ class)
egglib::Event::change_N (C++ class)
egglib::Event::change_R (C++ class)
egglib::Event::change_s (C++ class)
egglib::Event::copy (C++ function)
egglib::Event::date (C++ function)
egglib::Event::delayed (C++ class)
egglib::Event::disconnect (C++ function)
egglib::Event::Event (C++ function)
egglib::Event::event_type (C++ function)
egglib::Event::get_dest (C++ function)
egglib::Event::get_index (C++ function)
egglib::Event::get_number1 (C++ function)
egglib::Event::get_number2 (C++ function)
egglib::Event::get_param (C++ function)
egglib::Event::insert (C++ function)
egglib::Event::move (C++ function)
egglib::Event::next (C++ function)
egglib::Event::none (C++ class)
egglib::Event::perform (C++ function)
egglib::Event::prev (C++ function)
egglib::Event::set_dest (C++ function)
egglib::Event::set_index (C++ function)
egglib::Event::set_number1 (C++ function)
egglib::Event::set_number2 (C++ function)
egglib::Event::set_param (C++ function)
egglib::Event::Type (C++ type)
egglib::Export (C++ class)
egglib::Export::Export (C++ function)
egglib::Export::ms (C++ function)
egglib::Export::ms_auto_positions (C++ function)
egglib::Export::ms_num_positions (C++ function)
egglib::Export::ms_position (C++ function)
egglib::Export::newick (C++ function)
egglib::Export::~Export (C++ function)
egglib::FastaFormatter (C++ class)
egglib::FastaFormatter::defaults (C++ function)
egglib::FastaFormatter::FastaFormatter (C++ function)
egglib::FastaFormatter::set_first (C++ function)
egglib::FastaFormatter::set_labels (C++ function)
egglib::FastaFormatter::set_last (C++ function)
egglib::FastaFormatter::set_linelength (C++ function)
egglib::FastaFormatter::set_mapping (C++ function)
egglib::FastaFormatter::set_outgroup (C++ function)
egglib::FastaFormatter::set_shift_groups (C++ function)
egglib::FastaFormatter::write (C++ function)
egglib::FastaFormatter::write_string (C++ function)
egglib::FastaFormatter::~FastaFormatter (C++ function)
egglib::FastaParser (C++ class)
egglib::FastaParser::ch (C++ function)
egglib::FastaParser::clear (C++ function)
egglib::FastaParser::close (C++ function)
egglib::FastaParser::FastaParser (C++ function)
egglib::FastaParser::good (C++ function)
egglib::FastaParser::group (C++ function)
egglib::FastaParser::group_o (C++ function)
egglib::FastaParser::ls (C++ function)
egglib::FastaParser::name (C++ function)
egglib::FastaParser::ngroups (C++ function)
egglib::FastaParser::open_file (C++ function)
egglib::FastaParser::outgroup (C++ function)
egglib::FastaParser::read_all (C++ function)
egglib::FastaParser::read_sequence (C++ function)
egglib::FastaParser::reserve (C++ function)
egglib::FastaParser::set_stream (C++ function)
egglib::FastaParser::set_string (C++ function)
egglib::FastaParser::~FastaParser (C++ function)
egglib::Feature (C++ class)
egglib::Feature::clear (C++ function)
egglib::Feature::Feature (C++ function), [1]
egglib::Feature::get_Alias (C++ function)
egglib::Feature::get_attribute_key (C++ function)
egglib::Feature::get_attribute_value (C++ function)
egglib::Feature::get_Dbxref (C++ function)
egglib::Feature::get_Derives_from (C++ function)
egglib::Feature::get_end (C++ function)
egglib::Feature::get_Gap (C++ function)
egglib::Feature::get_ID (C++ function)
egglib::Feature::get_Is_circular (C++ function)
egglib::Feature::get_Name (C++ function)
egglib::Feature::get_Note (C++ function)
egglib::Feature::get_num_Alias (C++ function)
egglib::Feature::get_num_attributes (C++ function)
egglib::Feature::get_num_Dbxref (C++ function)
egglib::Feature::get_num_fragments (C++ function)
egglib::Feature::get_num_items_attribute (C++ function)
egglib::Feature::get_num_Note (C++ function)
egglib::Feature::get_num_Ontology_term (C++ function)
egglib::Feature::get_num_Parent (C++ function)
egglib::Feature::get_num_parents (C++ function)
egglib::Feature::get_num_parts (C++ function)
egglib::Feature::get_Ontology_term (C++ function)
egglib::Feature::get_parent (C++ function)
egglib::Feature::get_Parent (C++ function)
egglib::Feature::get_part (C++ function)
egglib::Feature::get_phase (C++ function)
egglib::Feature::get_score (C++ function)
egglib::Feature::get_seqid (C++ function)
egglib::Feature::get_source (C++ function)
egglib::Feature::get_start (C++ function)
egglib::Feature::get_strand (C++ function)
egglib::Feature::get_Target (C++ function)
egglib::Feature::get_type (C++ function)
egglib::Feature::minus (C++ class)
egglib::Feature::no_phase (C++ class)
egglib::Feature::no_strand (C++ class)
egglib::Feature::one (C++ class)
egglib::Feature::operator= (C++ function)
egglib::Feature::PHASE (C++ type)
egglib::Feature::plus (C++ class)
egglib::Feature::reset (C++ function)
egglib::Feature::set_Alias (C++ function)
egglib::Feature::set_attribute_key (C++ function)
egglib::Feature::set_attribute_value (C++ function)
egglib::Feature::set_Dbxref (C++ function)
egglib::Feature::set_Derives_from (C++ function)
egglib::Feature::set_end (C++ function)
egglib::Feature::set_Gap (C++ function)
egglib::Feature::set_ID (C++ function)
egglib::Feature::set_Is_circular (C++ function)
egglib::Feature::set_Name (C++ function)
egglib::Feature::set_Note (C++ function)
egglib::Feature::set_num_Alias (C++ function)
egglib::Feature::set_num_attributes (C++ function)
egglib::Feature::set_num_Dbxref (C++ function)
egglib::Feature::set_num_fragments (C++ function)
egglib::Feature::set_num_items_attribute (C++ function)
egglib::Feature::set_num_Note (C++ function)
egglib::Feature::set_num_Ontology_term (C++ function)
egglib::Feature::set_num_Parent (C++ function)
egglib::Feature::set_num_parents (C++ function)
egglib::Feature::set_num_parts (C++ function)
egglib::Feature::set_Ontology_term (C++ function)
egglib::Feature::set_parent (C++ function)
egglib::Feature::set_Parent (C++ function)
egglib::Feature::set_part (C++ function)
egglib::Feature::set_phase (C++ function)
egglib::Feature::set_score (C++ function)
egglib::Feature::set_seqid (C++ function)
egglib::Feature::set_source (C++ function)
egglib::Feature::set_start (C++ function)
egglib::Feature::set_strand (C++ function)
egglib::Feature::set_Target (C++ function)
egglib::Feature::set_type (C++ function)
egglib::Feature::STRAND (C++ type)
egglib::Feature::two (C++ class)
egglib::Feature::zero (C++ class)
egglib::Feature::~Feature (C++ function)
egglib::Filter (C++ class)
egglib::Filter::add_exploitable (C++ function)
egglib::Filter::add_exploitable_range (C++ function)
egglib::Filter::add_exploitable_with_alias (C++ function)
egglib::Filter::add_missing (C++ function)
egglib::Filter::add_missing_with_alias (C++ function)
egglib::Filter::check (C++ function)
egglib::Filter::clear (C++ function)
egglib::Filter::Filter (C++ function), [1]
egglib::Filter::is_exploitable (C++ function)
egglib::Filter::is_missing (C++ function)
egglib::Filter::operator= (C++ function)
egglib::Filter::reserve (C++ function)
egglib::Filter::~Filter (C++ function)
egglib::FreqHolder (C++ class)
egglib::FreqHolder::allele (C++ function)
egglib::FreqHolder::cluster_index (C++ function)
egglib::FreqHolder::FreqHolder (C++ function)
egglib::FreqHolder::frq_cluster (C++ function)
egglib::FreqHolder::frq_ingroup (C++ function)
egglib::FreqHolder::frq_outgroup (C++ function)
egglib::FreqHolder::frq_population (C++ function)
egglib::FreqHolder::genotype (C++ function)
egglib::FreqHolder::genotype_het (C++ function)
egglib::FreqHolder::genotype_item (C++ function)
egglib::FreqHolder::num_alleles (C++ function)
egglib::FreqHolder::num_clusters (C++ function)
egglib::FreqHolder::num_genotypes (C++ function)
egglib::FreqHolder::num_populations (C++ function)
egglib::FreqHolder::ploidy (C++ function)
egglib::FreqHolder::process_site (C++ function)
egglib::FreqHolder::process_vcf (C++ function)
egglib::FreqHolder::set_genotype_item (C++ function)
egglib::FreqHolder::set_nall (C++ function)
egglib::FreqHolder::setup_pop (C++ function)
egglib::FreqHolder::setup_raw (C++ function)
egglib::FreqHolder::setup_structure (C++ function)
egglib::FreqHolder::~FreqHolder (C++ function)
egglib::FreqSet (C++ class)
egglib::FreqSet::add_genotypes (C++ function)
egglib::FreqSet::FreqSet (C++ function)
egglib::FreqSet::frq_all (C++ function)
egglib::FreqSet::frq_gen (C++ function)
egglib::FreqSet::frq_het (C++ function)
egglib::FreqSet::incr_allele (C++ function)
egglib::FreqSet::incr_genotype (C++ function)
egglib::FreqSet::nieff (C++ function)
egglib::FreqSet::nseff (C++ function)
egglib::FreqSet::num_alleles (C++ function)
egglib::FreqSet::num_alleles_eff (C++ function)
egglib::FreqSet::num_genotypes (C++ function)
egglib::FreqSet::num_genotypes_eff (C++ function)
egglib::FreqSet::reset (C++ function)
egglib::FreqSet::setup (C++ function)
egglib::FreqSet::tell_het (C++ function)
egglib::FreqSet::tot_het (C++ function)
egglib::FreqSet::~FreqSet (C++ function)
egglib::Fs (C++ function)
egglib::GeneticCode (C++ class)
egglib::GeneticCode::aminoacid (C++ function)
egglib::GeneticCode::base (C++ function)
egglib::GeneticCode::codon (C++ function)
egglib::GeneticCode::diff1 (C++ function)
egglib::GeneticCode::diff2 (C++ function)
egglib::GeneticCode::diff3 (C++ function)
egglib::GeneticCode::GeneticCode (C++ function), [1]
egglib::GeneticCode::get_code (C++ function)
egglib::GeneticCode::int2codon (C++ function)
egglib::GeneticCode::name (C++ function)
egglib::GeneticCode::ndiff (C++ function)
egglib::GeneticCode::NSsites (C++ function), [1], [2]
egglib::GeneticCode::num_codes (C++ function)
egglib::GeneticCode::set_code (C++ function)
egglib::GeneticCode::Ssites (C++ function), [1], [2]
egglib::GeneticCode::start (C++ function)
egglib::GeneticCode::translate (C++ function)
egglib::GFF3 (C++ class)
egglib::GFF3::clear (C++ function)
egglib::GFF3::feature (C++ function)
egglib::GFF3::gene (C++ function)
egglib::GFF3::GFF3 (C++ function)
egglib::GFF3::liberal (C++ function)
egglib::GFF3::metadata_key (C++ function)
egglib::GFF3::metadata_value (C++ function)
egglib::GFF3::num_features (C++ function)
egglib::GFF3::num_genes (C++ function)
egglib::GFF3::num_metadata (C++ function)
egglib::GFF3::parse (C++ function), [1]
egglib::GFF3::parse_string (C++ function)
egglib::GFF3::reset (C++ function)
egglib::GFF3::sequences (C++ function)
egglib::GFF3::~GFF3 (C++ function)
egglib::Haplotypes (C++ class)
egglib::Haplotypes::cp_dist (C++ function)
egglib::Haplotypes::cp_haplotypes (C++ function)
egglib::Haplotypes::cp_stats (C++ function)
egglib::Haplotypes::dist (C++ function)
egglib::Haplotypes::freq_i (C++ function)
egglib::Haplotypes::freq_o (C++ function)
egglib::Haplotypes::Fst (C++ function)
egglib::Haplotypes::get_site (C++ function)
egglib::Haplotypes::hapl (C++ function)
egglib::Haplotypes::Haplotypes (C++ function)
egglib::Haplotypes::impute (C++ function)
egglib::Haplotypes::Kst (C++ function)
egglib::Haplotypes::load (C++ function)
egglib::Haplotypes::map_sample (C++ function)
egglib::Haplotypes::mis_idx (C++ function)
egglib::Haplotypes::n_ing (C++ function)
egglib::Haplotypes::n_mis (C++ function)
egglib::Haplotypes::n_missing (C++ function)
egglib::Haplotypes::n_otg (C++ function)
egglib::Haplotypes::n_pop (C++ function)
egglib::Haplotypes::n_potential (C++ function)
egglib::Haplotypes::n_sam (C++ function)
egglib::Haplotypes::n_sites (C++ function)
egglib::Haplotypes::ne_ing (C++ function)
egglib::Haplotypes::ne_otg (C++ function)
egglib::Haplotypes::ne_pop (C++ function)
egglib::Haplotypes::ng_hapl (C++ function)
egglib::Haplotypes::ni_hapl (C++ function)
egglib::Haplotypes::nstot (C++ function)
egglib::Haplotypes::nt_hapl (C++ function)
egglib::Haplotypes::potential (C++ function)
egglib::Haplotypes::prepare_impute (C++ function)
egglib::Haplotypes::resolve (C++ function)
egglib::Haplotypes::set_struct (C++ function)
egglib::Haplotypes::setup (C++ function)
egglib::Haplotypes::Snn (C++ function)
egglib::Haplotypes::~Haplotypes (C++ function)
egglib::IntersperseAlign (C++ class)
egglib::IntersperseAlign::get_positions (C++ function)
egglib::IntersperseAlign::intersperse (C++ function)
egglib::IntersperseAlign::IntersperseAlign (C++ function)
egglib::IntersperseAlign::load (C++ function)
egglib::IntersperseAlign::set_allele (C++ function)
egglib::IntersperseAlign::set_length (C++ function)
egglib::IntersperseAlign::set_num_alleles (C++ function)
egglib::IntersperseAlign::set_position (C++ function)
egglib::IntersperseAlign::set_random (C++ function)
egglib::IntersperseAlign::set_round_position (C++ function)
egglib::IntersperseAlign::~IntersperseAlign (C++ function)
egglib::Lineage (C++ class)
egglib::Lineage::addTree (C++ function)
egglib::Lineage::cov (C++ function)
egglib::Lineage::get_node (C++ function)
egglib::Lineage::Lineage (C++ function)
egglib::Lineage::reset (C++ function)
egglib::Lineage::set_node (C++ function)
egglib::Lineage::~Lineage (C++ function)
egglib::MatrixLD (C++ class)
egglib::MatrixLD::computeLD (C++ function)
egglib::MatrixLD::computeRmin (C++ function)
egglib::MatrixLD::computeStats (C++ function)
egglib::MatrixLD::distance (C++ function)
egglib::MatrixLD::ignore (C++ class)
egglib::MatrixLD::index1 (C++ function)
egglib::MatrixLD::index2 (C++ function)
egglib::MatrixLD::load (C++ function)
egglib::MatrixLD::MatrixLD (C++ function)
egglib::MatrixLD::MultiAllelic (C++ type)
egglib::MatrixLD::num_allele_pairs (C++ function)
egglib::MatrixLD::num_allele_pairs_adj (C++ function)
egglib::MatrixLD::num_alleles (C++ function)
egglib::MatrixLD::num_pairs (C++ function)
egglib::MatrixLD::num_tot (C++ function)
egglib::MatrixLD::pairLD (C++ function)
egglib::MatrixLD::process (C++ function)
egglib::MatrixLD::reset (C++ function)
egglib::MatrixLD::Rmin (C++ function)
egglib::MatrixLD::Rmin_left (C++ function)
egglib::MatrixLD::Rmin_num_sites (C++ function)
egglib::MatrixLD::Rmin_right (C++ function)
egglib::MatrixLD::toggle_off (C++ function)
egglib::MatrixLD::toggle_Rmin (C++ function)
egglib::MatrixLD::toggle_stats (C++ function)
egglib::MatrixLD::use_all (C++ class)
egglib::MatrixLD::use_main (C++ class)
egglib::MatrixLD::Za (C++ function)
egglib::MatrixLD::ZnS (C++ function)
egglib::MatrixLD::ZnS_star1 (C++ function)
egglib::MatrixLD::ZnS_star2 (C++ function)
egglib::MatrixLD::ZZ (C++ function)
egglib::MatrixLD::~MatrixLD (C++ function)
egglib::Migration (C++ class)
egglib::Migration::get_pair (C++ function)
egglib::Migration::get_row (C++ function)
egglib::Migration::Migration (C++ function)
egglib::Migration::n (C++ function)
egglib::Migration::restore (C++ function)
egglib::Migration::set_all (C++ function)
egglib::Migration::set_all_R (C++ function)
egglib::Migration::set_pair (C++ function)
egglib::Migration::set_pair_R (C++ function)
egglib::Migration::set_row (C++ function)
egglib::Migration::set_row_R (C++ function)
egglib::Migration::~Migration (C++ function)
egglib::nnet::Data (C++ class)
egglib::nnet::Data::Data (C++ function), [1]
egglib::nnet::Data::get_input (C++ function)
egglib::nnet::Data::get_num_input (C++ function)
egglib::nnet::Data::get_num_output (C++ function)
egglib::nnet::Data::get_num_patterns (C++ function)
egglib::nnet::Data::get_output (C++ function)
egglib::nnet::Data::mean_input (C++ function)
egglib::nnet::Data::mean_output (C++ function)
egglib::nnet::Data::normalize (C++ function)
egglib::nnet::Data::normalize_input (C++ function)
egglib::nnet::Data::normalize_output (C++ function)
egglib::nnet::Data::operator= (C++ function)
egglib::nnet::Data::set_input (C++ function)
egglib::nnet::Data::set_num_input (C++ function)
egglib::nnet::Data::set_num_output (C++ function)
egglib::nnet::Data::set_num_patterns (C++ function)
egglib::nnet::Data::set_output (C++ function)
egglib::nnet::Data::std_input (C++ function)
egglib::nnet::Data::std_output (C++ function)
egglib::nnet::Data::unnormalize_output (C++ function)
egglib::nnet::Data::~Data (C++ function)
egglib::nnet::Network (C++ class)
egglib::nnet::Network::init_weights (C++ function)
egglib::nnet::Network::Network (C++ function)
egglib::nnet::Network::num_iter (C++ function)
egglib::nnet::Network::predict (C++ function)
egglib::nnet::Network::prediction (C++ function)
egglib::nnet::Network::setup (C++ function)
egglib::nnet::Network::testing_error (C++ function)
egglib::nnet::Network::train (C++ function)
egglib::nnet::Network::training_error (C++ function)
egglib::nnet::Network::weight_hidden (C++ function), [1]
egglib::nnet::Network::weight_output (C++ function), [1]
egglib::nnet::Network::~Network (C++ function)
egglib::nnet::Neuron (C++ class)
egglib::nnet::Neuron::activate (C++ function)
egglib::nnet::Neuron::config (C++ function)
egglib::nnet::Neuron::delta (C++ function)
egglib::nnet::Neuron::get_output (C++ function)
egglib::nnet::Neuron::get_weight (C++ function)
egglib::nnet::Neuron::Neuron (C++ function)
egglib::nnet::Neuron::propagate (C++ function)
egglib::nnet::Neuron::set_input (C++ function)
egglib::nnet::Neuron::set_weight (C++ function)
egglib::nnet::Neuron::update (C++ function)
egglib::nnet::Neuron::~Neuron (C++ function)
egglib::Node (C++ class)
egglib::Node::addMutation (C++ function)
egglib::Node::clear_mutations (C++ function)
egglib::Node::date (C++ function)
egglib::Node::get_L (C++ function)
egglib::Node::is_terminal (C++ function)
egglib::Node::label (C++ function)
egglib::Node::mutationPos (C++ function)
egglib::Node::mutationSite (C++ function)
egglib::Node::nmut (C++ function)
egglib::Node::Node (C++ function), [1]
egglib::Node::operator= (C++ function)
egglib::Node::reset (C++ function)
egglib::Node::set_internal (C++ function)
egglib::Node::set_L (C++ function)
egglib::Node::set_terminal (C++ function)
egglib::Node::son1 (C++ function)
egglib::Node::son2 (C++ function)
egglib::Node::~Node (C++ function)
egglib::PairwiseLD (C++ class)
egglib::PairwiseLD::compute (C++ function)
egglib::PairwiseLD::D (C++ function)
egglib::PairwiseLD::Dp (C++ function)
egglib::PairwiseLD::freq (C++ function)
egglib::PairwiseLD::freq1 (C++ function)
egglib::PairwiseLD::freq2 (C++ function)
egglib::PairwiseLD::index1 (C++ function)
egglib::PairwiseLD::index2 (C++ function)
egglib::PairwiseLD::nsam (C++ function)
egglib::PairwiseLD::num_alleles1 (C++ function)
egglib::PairwiseLD::num_alleles2 (C++ function)
egglib::PairwiseLD::PairwiseLD (C++ function)
egglib::PairwiseLD::process (C++ function)
egglib::PairwiseLD::r (C++ function)
egglib::PairwiseLD::reset (C++ function)
egglib::PairwiseLD::rsq (C++ function)
egglib::PairwiseLD::~PairwiseLD (C++ function)
egglib::ParalogPi (C++ class)
egglib::ParalogPi::load (C++ function)
egglib::ParalogPi::num_paralogs (C++ function)
egglib::ParalogPi::num_samples (C++ function)
egglib::ParalogPi::num_sites_pair (C++ function)
egglib::ParalogPi::num_sites_paralog (C++ function)
egglib::ParalogPi::num_sites_tot (C++ function)
egglib::ParalogPi::ParalogPi (C++ function)
egglib::ParalogPi::Pib (C++ function)
egglib::ParalogPi::Piw (C++ function)
egglib::ParalogPi::reset (C++ function)
egglib::ParalogPi::~ParalogPi (C++ function)
egglib::Params (C++ class)
egglib::Params::addChange (C++ function)
egglib::Params::autoSitePos (C++ function)
egglib::Params::clearChanges (C++ function)
egglib::Params::firstChange (C++ function)
egglib::Params::G_R (C++ function)
egglib::Params::get_fixed (C++ function)
egglib::Params::get_G (C++ function)
egglib::Params::get_K (C++ function)
egglib::Params::get_L (C++ function)
egglib::Params::get_max_iter (C++ function)
egglib::Params::get_mutmodel (C++ function)
egglib::Params::get_N (C++ function)
egglib::Params::get_n1 (C++ function)
egglib::Params::get_n2 (C++ function)
egglib::Params::get_outgroup (C++ function)
egglib::Params::get_R (C++ function)
egglib::Params::get_random_start_allele (C++ function)
egglib::Params::get_s (C++ function)
egglib::Params::get_sitePos (C++ function)
egglib::Params::get_siteW (C++ function)
egglib::Params::get_theta (C++ function)
egglib::Params::get_TPMparam (C++ function)
egglib::Params::get_TPMproba (C++ function)
egglib::Params::get_transW_matrix (C++ function)
egglib::Params::get_transW_pair (C++ function)
egglib::Params::get_transW_row (C++ function)
egglib::Params::IAM (C++ class)
egglib::Params::k (C++ function)
egglib::Params::KAM (C++ class)
egglib::Params::lastChange (C++ function)
egglib::Params::M (C++ function)
egglib::Params::MutationModel (C++ type)
egglib::Params::N_R (C++ function)
egglib::Params::nDSChanges (C++ function)
egglib::Params::nextChangeDate (C++ function)
egglib::Params::nextChangeDo (C++ function)
egglib::Params::numChanges (C++ function)
egglib::Params::Params (C++ function), [1]
egglib::Params::R_R (C++ function)
egglib::Params::restore (C++ function)
egglib::Params::s_R (C++ function)
egglib::Params::set_fixed (C++ function)
egglib::Params::set_G (C++ function)
egglib::Params::set_K (C++ function)
egglib::Params::set_L (C++ function)
egglib::Params::set_max_iter (C++ function)
egglib::Params::set_mutmodel (C++ function)
egglib::Params::set_N (C++ function)
egglib::Params::set_n1 (C++ function)
egglib::Params::set_n2 (C++ function)
egglib::Params::set_outgroup (C++ function)
egglib::Params::set_R (C++ function)
egglib::Params::set_random_start_allele (C++ function)
egglib::Params::set_s (C++ function)
egglib::Params::set_sitePos (C++ function)
egglib::Params::set_siteW (C++ function)
egglib::Params::set_theta (C++ function)
egglib::Params::set_TPMparam (C++ function)
egglib::Params::set_TPMproba (C++ function)
egglib::Params::set_transW_matrix (C++ function)
egglib::Params::set_transW_pair (C++ function)
egglib::Params::SMM (C++ class)
egglib::Params::summary (C++ function)
egglib::Params::totalSiteW (C++ function)
egglib::Params::TPM (C++ class)
egglib::Params::validate (C++ function)
egglib::Params::~Params (C++ function)
egglib::Random (C++ class)
egglib::Random::binomrand (C++ function)
egglib::Random::brand (C++ function)
egglib::Random::erand (C++ function)
egglib::Random::get_seed (C++ function)
egglib::Random::grand (C++ function)
egglib::Random::irand (C++ function)
egglib::Random::nrand (C++ function)
egglib::Random::prand (C++ function)
egglib::Random::rand_int32 (C++ function)
egglib::Random::Random (C++ function), [1]
egglib::Random::set_seed (C++ function)
egglib::Random::uniform (C++ function)
egglib::Random::uniform53 (C++ function)
egglib::Random::uniformcl (C++ function)
egglib::Random::uniformop (C++ function)
egglib::Random::~Random (C++ function)
egglib::Rd (C++ class)
egglib::Rd::compute (C++ function)
egglib::Rd::load (C++ function)
egglib::Rd::Rd (C++ function)
egglib::Rd::reset (C++ function)
egglib::Rd::~Rd (C++ function)
egglib::read_fasta_file (C++ function)
egglib::read_fasta_string (C++ function)
egglib::SiteDiversity (C++ class)
egglib::SiteDiversity::a (C++ function)
egglib::SiteDiversity::a0 (C++ function)
egglib::SiteDiversity::Aglob (C++ function)
egglib::SiteDiversity::Aing (C++ function)
egglib::SiteDiversity::Aout (C++ function)
egglib::SiteDiversity::average (C++ function)
egglib::SiteDiversity::b (C++ function)
egglib::SiteDiversity::b1 (C++ function)
egglib::SiteDiversity::b2 (C++ function)
egglib::SiteDiversity::c (C++ function)
egglib::SiteDiversity::c0 (C++ function)
egglib::SiteDiversity::D (C++ function)
egglib::SiteDiversity::d (C++ function)
egglib::SiteDiversity::derived (C++ function)
egglib::SiteDiversity::flag (C++ function)
egglib::SiteDiversity::global_allele (C++ function)
egglib::SiteDiversity::Gst (C++ function)
egglib::SiteDiversity::Gste (C++ function)
egglib::SiteDiversity::He (C++ function)
egglib::SiteDiversity::He_pop (C++ function)
egglib::SiteDiversity::Hi (C++ function)
egglib::SiteDiversity::Ho (C++ function)
egglib::SiteDiversity::Hst (C++ function)
egglib::SiteDiversity::k (C++ function)
egglib::SiteDiversity::n (C++ function)
egglib::SiteDiversity::nclu_eff (C++ function)
egglib::SiteDiversity::npop_eff1 (C++ function)
egglib::SiteDiversity::npop_eff2 (C++ function)
egglib::SiteDiversity::npop_eff3 (C++ function)
egglib::SiteDiversity::ns (C++ function)
egglib::SiteDiversity::nsites1 (C++ function)
egglib::SiteDiversity::nsites10 (C++ function)
egglib::SiteDiversity::nsites11 (C++ function)
egglib::SiteDiversity::nsites12 (C++ function)
egglib::SiteDiversity::nsites2 (C++ function)
egglib::SiteDiversity::nsites3 (C++ function)
egglib::SiteDiversity::nsites4 (C++ function)
egglib::SiteDiversity::nsites5 (C++ function)
egglib::SiteDiversity::nsites6 (C++ function)
egglib::SiteDiversity::nsites7 (C++ function)
egglib::SiteDiversity::nsites8 (C++ function)
egglib::SiteDiversity::nsites9 (C++ function)
egglib::SiteDiversity::orientable (C++ function)
egglib::SiteDiversity::pairdiff (C++ function)
egglib::SiteDiversity::pairdiff_inter (C++ function)
egglib::SiteDiversity::process (C++ function)
egglib::SiteDiversity::R (C++ function)
egglib::SiteDiversity::reset (C++ function)
egglib::SiteDiversity::S (C++ function)
egglib::SiteDiversity::Sd (C++ function)
egglib::SiteDiversity::SiteDiversity (C++ function)
egglib::SiteDiversity::thetaIAM (C++ function)
egglib::SiteDiversity::thetaSMM (C++ function)
egglib::SiteDiversity::toggle_fstats_diplo (C++ function)
egglib::SiteDiversity::toggle_fstats_haplo (C++ function)
egglib::SiteDiversity::toggle_fstats_hier (C++ function)
egglib::SiteDiversity::toggle_hstats (C++ function)
egglib::SiteDiversity::toggle_off (C++ function)
egglib::SiteDiversity::~SiteDiversity (C++ function)
egglib::SiteGeno (C++ class)
egglib::SiteGeno::homoz (C++ function)
egglib::SiteGeno::process (C++ function)
egglib::SiteHolder (C++ class)
egglib::SiteHolder::add_ing (C++ function)
egglib::SiteHolder::add_otg (C++ function)
egglib::SiteHolder::get_allele (C++ function)
egglib::SiteHolder::get_i (C++ function)
egglib::SiteHolder::get_missing (C++ function)
egglib::SiteHolder::get_missing_ing (C++ function)
egglib::SiteHolder::get_missing_otg (C++ function)
egglib::SiteHolder::get_nall (C++ function)
egglib::SiteHolder::get_nall_ing (C++ function)
egglib::SiteHolder::get_ning (C++ function)
egglib::SiteHolder::get_nout (C++ function)
egglib::SiteHolder::get_o (C++ function)
egglib::SiteHolder::get_pi (C++ function)
egglib::SiteHolder::get_ploidy (C++ function)
egglib::SiteHolder::get_po (C++ function)
egglib::SiteHolder::get_straight_i (C++ function)
egglib::SiteHolder::get_straight_o (C++ function)
egglib::SiteHolder::get_tot_missing (C++ function)
egglib::SiteHolder::load_ing (C++ function)
egglib::SiteHolder::load_otg (C++ function)
egglib::SiteHolder::process_align (C++ function)
egglib::SiteHolder::process_vcf (C++ function)
egglib::SiteHolder::reset (C++ function)
egglib::SiteHolder::set_allele (C++ function)
egglib::SiteHolder::set_i (C++ function)
egglib::SiteHolder::set_nall (C++ function)
egglib::SiteHolder::set_o (C++ function)
egglib::SiteHolder::SiteHolder (C++ function)
egglib::SiteHolder::~SiteHolder (C++ function)
egglib::stirling_table (C++ function)
egglib::StructureCluster (C++ class)
egglib::StructureCluster::add_indiv (C++ function)
egglib::StructureCluster::add_pop (C++ function)
egglib::StructureCluster::add_sample (C++ function)
egglib::StructureCluster::get_indiv (C++ function)
egglib::StructureCluster::get_label (C++ function)
egglib::StructureCluster::get_population (C++ function)
egglib::StructureCluster::num_indiv (C++ function)
egglib::StructureCluster::num_pop (C++ function)
egglib::StructureCluster::reset (C++ function)
egglib::StructureHolder (C++ class)
egglib::StructureHolder::add_cluster (C++ function)
egglib::StructureHolder::add_individual_ingroup (C++ function)
egglib::StructureHolder::add_individual_outgroup (C++ function)
egglib::StructureHolder::add_pop_filter (C++ function)
egglib::StructureHolder::add_population (C++ function)
egglib::StructureHolder::add_sample_ingroup (C++ function)
egglib::StructureHolder::add_sample_outgroup (C++ function)
egglib::StructureHolder::check_ploidy (C++ function)
egglib::StructureHolder::get_cluster (C++ function)
egglib::StructureHolder::get_indiv_ingroup (C++ function)
egglib::StructureHolder::get_indiv_outgroup (C++ function)
egglib::StructureHolder::get_no (C++ function)
egglib::StructureHolder::get_no_req (C++ function)
egglib::StructureHolder::get_ns (C++ function)
egglib::StructureHolder::get_ns_req (C++ function)
egglib::StructureHolder::get_ploidy (C++ function)
egglib::StructureHolder::get_pop_index (C++ function)
egglib::StructureHolder::get_population (C++ function)
egglib::StructureHolder::get_structure (C++ function)
egglib::StructureHolder::num_clust (C++ function)
egglib::StructureHolder::num_indiv_ingroup (C++ function)
egglib::StructureHolder::num_indiv_outgroup (C++ function)
egglib::StructureHolder::num_pop (C++ function)
egglib::StructureHolder::process_ingroup (C++ function)
egglib::StructureHolder::process_outgroup (C++ function)
egglib::StructureHolder::reserve_filter (C++ function)
egglib::StructureHolder::reset (C++ function)
egglib::StructureHolder::reset_filter (C++ function)
egglib::StructureIndiv (C++ class)
egglib::StructureIndiv::add_sample (C++ function)
egglib::StructureIndiv::get_cluster (C++ function)
egglib::StructureIndiv::get_label (C++ function)
egglib::StructureIndiv::get_population (C++ function)
egglib::StructureIndiv::get_sample (C++ function)
egglib::StructureIndiv::num_samples (C++ function)
egglib::StructureIndiv::reset (C++ function)
egglib::StructurePopulation (C++ class)
egglib::StructurePopulation::add_indiv (C++ function)
egglib::StructurePopulation::add_sample (C++ function)
egglib::StructurePopulation::get_cluster (C++ function)
egglib::StructurePopulation::get_indiv (C++ function)
egglib::StructurePopulation::get_label (C++ function)
egglib::StructurePopulation::num_indiv (C++ function)
egglib::StructurePopulation::reset (C++ function)
egglib::Tree (C++ class)
egglib::Tree::addNode (C++ function)
egglib::Tree::clear_mutations (C++ function)
egglib::Tree::coal (C++ function)
egglib::Tree::cov (C++ function)
egglib::Tree::L (C++ function)
egglib::Tree::mutate (C++ function)
egglib::Tree::nnodes (C++ function)
egglib::Tree::node (C++ function)
egglib::Tree::operator= (C++ function)
egglib::Tree::recomb (C++ function)
egglib::Tree::reset (C++ function)
egglib::Tree::root (C++ function)
egglib::Tree::start (C++ function)
egglib::Tree::stop (C++ function)
egglib::Tree::Tree (C++ function), [1]
egglib::Tree::~Tree (C++ function)
egglib::vcf::Alt (C++ class)
egglib::vcf::Alt::Alt (C++ function), [1], [2], [3]
egglib::vcf::Alt::operator= (C++ function), [1]
egglib::vcf::Alt::~Alt (C++ function)
egglib::vcf::Filter (C++ class)
egglib::vcf::Filter::clear (C++ function)
egglib::vcf::Filter::Filter (C++ function), [1], [2]
egglib::vcf::Filter::get_description (C++ function)
egglib::vcf::Filter::get_extra_key (C++ function)
egglib::vcf::Filter::get_extra_value (C++ function)
egglib::vcf::Filter::get_ID (C++ function)
egglib::vcf::Filter::get_num_extra (C++ function)
egglib::vcf::Filter::operator= (C++ function)
egglib::vcf::Filter::set_description (C++ function)
egglib::vcf::Filter::set_extra (C++ function)
egglib::vcf::Filter::set_ID (C++ function)
egglib::vcf::Filter::update (C++ function)
egglib::vcf::Filter::~Filter (C++ function)
egglib::vcf::FlagInfo (C++ class)
egglib::vcf::FlagInfo::FlagInfo (C++ function), [1]
egglib::vcf::FlagInfo::get_ID (C++ function)
egglib::vcf::FlagInfo::operator= (C++ function)
egglib::vcf::FlagInfo::set_ID (C++ function)
egglib::vcf::FlagInfo::~FlagInfo (C++ function)
egglib::vcf::Format (C++ class)
egglib::vcf::Format::Format (C++ function), [1], [2], [3]
egglib::vcf::Format::get_type (C++ function)
egglib::vcf::Format::operator= (C++ function), [1]
egglib::vcf::Format::set_type (C++ function)
egglib::vcf::Format::update (C++ function)
egglib::vcf::Info (C++ class)
egglib::vcf::Info::Character (C++ class)
egglib::vcf::Info::Flag (C++ class)
egglib::vcf::Info::Float (C++ class)
egglib::vcf::Info::get_number (C++ function)
egglib::vcf::Info::get_type (C++ function)
egglib::vcf::Info::Info (C++ function), [1], [2]
egglib::vcf::Info::Integer (C++ class)
egglib::vcf::Info::operator= (C++ function)
egglib::vcf::Info::set_number (C++ function)
egglib::vcf::Info::set_type (C++ function)
egglib::vcf::Info::String (C++ class)
egglib::vcf::Info::Type (C++ type)
egglib::vcf::Info::update (C++ function)
egglib::vcf::Meta (C++ class)
egglib::vcf::Meta::clear (C++ function)
egglib::vcf::Meta::get_key (C++ function)
egglib::vcf::Meta::get_value (C++ function)
egglib::vcf::Meta::Meta (C++ function), [1], [2]
egglib::vcf::Meta::operator= (C++ function)
egglib::vcf::Meta::set_key (C++ function)
egglib::vcf::Meta::set_value (C++ function)
egglib::vcf::Meta::update (C++ function)
egglib::vcf::Meta::~Meta (C++ function)
egglib::vcf::SampleInfo (C++ class)
egglib::vcf::SampleInfo::CharacterItem (C++ function)
egglib::vcf::SampleInfo::clear (C++ function)
egglib::vcf::SampleInfo::FloatItem (C++ function)
egglib::vcf::SampleInfo::IntegerItem (C++ function)
egglib::vcf::SampleInfo::num_CharacterEntries (C++ function)
egglib::vcf::SampleInfo::num_CharacterItems (C++ function)
egglib::vcf::SampleInfo::num_FloatEntries (C++ function)
egglib::vcf::SampleInfo::num_FloatItems (C++ function)
egglib::vcf::SampleInfo::num_IntegerEntries (C++ function)
egglib::vcf::SampleInfo::num_IntegerItems (C++ function)
egglib::vcf::SampleInfo::num_StringEntries (C++ function)
egglib::vcf::SampleInfo::num_StringItems (C++ function)
egglib::vcf::SampleInfo::operator= (C++ function)
egglib::vcf::SampleInfo::reset (C++ function)
egglib::vcf::SampleInfo::SampleInfo (C++ function), [1]
egglib::vcf::SampleInfo::StringItem (C++ function)
egglib::vcf::SampleInfo::~SampleInfo (C++ function)
egglib::vcf::StringInfo (C++ class)
egglib::vcf::StringInfo::change (C++ function)
egglib::vcf::StringInfo::operator= (C++ function)
egglib::vcf::StringInfo::StringInfo (C++ function), [1]
egglib::vcf::StringInfo::~StringInfo (C++ function)
egglib::vcf::TypeInfo (C++ class)
egglib::vcf::TypeInfo::get_expected_number (C++ function)
egglib::vcf::TypeInfo::item (C++ function)
egglib::vcf::TypeInfo::num_items (C++ function)
egglib::vcf::TypeInfo::operator= (C++ function)
egglib::vcf::TypeInfo::reset (C++ function)
egglib::vcf::TypeInfo::set_expected_number (C++ function)
egglib::vcf::TypeInfo::TypeInfo (C++ function), [1]
egglib::vcf::TypeInfo::~TypeInfo (C++ function)
egglib::VcfParser (C++ class)
egglib::VcfParser::AA_index (C++ function)
egglib::VcfParser::AA_string (C++ function)
egglib::VcfParser::AC (C++ function)
egglib::VcfParser::add_alt (C++ function)
egglib::VcfParser::add_filter (C++ function)
egglib::VcfParser::add_format (C++ function)
egglib::VcfParser::add_info (C++ function)
egglib::VcfParser::add_meta (C++ function)
egglib::VcfParser::AF (C++ function)
egglib::VcfParser::allow_gap (C++ function)
egglib::VcfParser::allow_X (C++ function)
egglib::VcfParser::alternate (C++ function)
egglib::VcfParser::alternate_type (C++ function)
egglib::VcfParser::AN (C++ function)
egglib::VcfParser::CharacterInfo (C++ function)
egglib::VcfParser::chromosome (C++ function)
egglib::VcfParser::clear (C++ function)
egglib::VcfParser::clear_stream (C++ function)
egglib::VcfParser::failed_test (C++ function)
egglib::VcfParser::field (C++ function)
egglib::VcfParser::field_index (C++ function)
egglib::VcfParser::field_rank (C++ function), [1]
egglib::VcfParser::file_end (C++ function)
egglib::VcfParser::file_format (C++ function)
egglib::VcfParser::find_alt (C++ function)
egglib::VcfParser::find_filter (C++ function)
egglib::VcfParser::find_format (C++ function)
egglib::VcfParser::find_info (C++ function)
egglib::VcfParser::find_meta (C++ function)
egglib::VcfParser::FlagInfo (C++ function)
egglib::VcfParser::FloatInfo (C++ function)
egglib::VcfParser::get_alt (C++ function)
egglib::VcfParser::get_filter (C++ function)
egglib::VcfParser::get_format (C++ function)
egglib::VcfParser::get_idx_frt_sample (C++ function)
egglib::VcfParser::get_index (C++ function)
egglib::VcfParser::get_info (C++ function)
egglib::VcfParser::get_meta (C++ function)
egglib::VcfParser::get_sample (C++ function)
egglib::VcfParser::good (C++ function)
egglib::VcfParser::GT (C++ function)
egglib::VcfParser::GT_phased (C++ function), [1]
egglib::VcfParser::GT_ploidy (C++ function)
egglib::VcfParser::has_AA (C++ function)
egglib::VcfParser::has_AC (C++ function)
egglib::VcfParser::has_AF (C++ function)
egglib::VcfParser::has_AN (C++ function)
egglib::VcfParser::has_data (C++ function)
egglib::VcfParser::has_GT (C++ function)
egglib::VcfParser::has_index (C++ function)
egglib::VcfParser::has_PL (C++ function)
egglib::VcfParser::ID (C++ function)
egglib::VcfParser::index_fname (C++ function)
egglib::VcfParser::IntegerInfo (C++ function)
egglib::VcfParser::len_reference (C++ function)
egglib::VcfParser::num_AC (C++ function)
egglib::VcfParser::num_AF (C++ function)
egglib::VcfParser::num_alt (C++ function)
egglib::VcfParser::num_alternate (C++ function)
egglib::VcfParser::num_CharacterInfo (C++ function)
egglib::VcfParser::num_failed_tests (C++ function)
egglib::VcfParser::num_fields (C++ function)
egglib::VcfParser::num_filter (C++ function)
egglib::VcfParser::num_FlagInfo (C++ function)
egglib::VcfParser::num_FloatInfo (C++ function)
egglib::VcfParser::num_format (C++ function)
egglib::VcfParser::num_ID (C++ function)
egglib::VcfParser::num_info (C++ function)
egglib::VcfParser::num_IntegerInfo (C++ function)
egglib::VcfParser::num_meta (C++ function)
egglib::VcfParser::num_samples (C++ function)
egglib::VcfParser::num_StringInfo (C++ function)
egglib::VcfParser::open_file (C++ function)
egglib::VcfParser::position (C++ function)
egglib::VcfParser::quality (C++ function)
egglib::VcfParser::read (C++ function)
egglib::VcfParser::read_header (C++ function)
egglib::VcfParser::read_index (C++ function)
egglib::VcfParser::read_line (C++ function)
egglib::VcfParser::reference (C++ function)
egglib::VcfParser::reset (C++ function)
egglib::VcfParser::reset_variant (C++ function)
egglib::VcfParser::rewind (C++ function)
egglib::VcfParser::sample_info (C++ function)
egglib::VcfParser::set_currline (C++ function)
egglib::VcfParser::set_index (C++ function)
egglib::VcfParser::set_previous_next (C++ function)
egglib::VcfParser::set_stream (C++ function)
egglib::VcfParser::StringInfo (C++ function)
egglib::VcfParser::unread (C++ function)
egglib::VcfParser::VcfParser (C++ function)
egglib::VcfParser::~VcfParser (C++ function)
egglib::VectorInt (C++ class)
egglib::VectorInt::clear (C++ function)
egglib::VectorInt::get_item (C++ function)
egglib::VectorInt::get_num_values (C++ function)
egglib::VectorInt::operator= (C++ function)
egglib::VectorInt::set_item (C++ function)
egglib::VectorInt::set_num_values (C++ function)
egglib::VectorInt::VectorInt (C++ function), [1]
egglib::VectorInt::~VectorInt (C++ function)
EHH (class in egglib.stats)
encode() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
end (egglib.io.GFF3Feature attribute)
end_position (egglib.io._vcf.VcfWindow attribute)
equalize() (egglib.Container method)
EventList (class in egglib.coalesce)
exon_index() (egglib.tools.ReadingFrame method)
exploitable() (egglib.stats.Filter method)
exponential() (egglib.tools.Random method)
extract() (egglib.Align method)
(egglib.Tree method)
(egglib.io.GenBank method)

F

failed_tests (egglib.io.Variant attribute)
fasta_iter (class in egglib.io)
feature_iter() (egglib.io.GFF3 method)
file_format (egglib.io.VcfParser attribute)
Filter (class in egglib.stats)
filter() (egglib.Align method)
filter_amino (in module egglib.stats)
filter_codon (in module egglib.stats), [1]
filter_default (in module egglib.stats)
filter_dna (in module egglib.stats)
filter_num (in module egglib.stats)
filter_rna (in module egglib.stats)
filter_ssr (in module egglib.stats)
filter_strict (in module egglib.stats)
find() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
(egglib.SequenceView method)
find_clade() (egglib.Tree method)
find_motif() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
find_motif_o() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
fix_ends() (egglib.Align method)
fname (egglib.misc.TempFile attribute)
format_fields (egglib.io.Variant attribute)
Freq (class in egglib.stats)
freq_allele() (egglib.stats.Freq method)
freq_from_list() (in module egglib.stats)
freq_from_site() (in module egglib.stats)
freq_from_vcf() (in module egglib.stats)
freq_genotype() (egglib.stats.Freq method)
frequency_nodes() (egglib.Tree method)
from_clustal() (in module egglib.io)
from_fasta() (in module egglib.io)
from_genalys() (in module egglib.io)
from_header() (egglib.io.VcfParser class method)
from_staden() (in module egglib.io)

G

gap (egglib.io.GFF3Feature attribute)
GenBank (class in egglib.io)
GenBankFeature (class in egglib.io)
GenBankFeatureLocation (class in egglib.io)
genotype() (egglib.stats.Freq method)
geometric() (egglib.tools.Random method)
get() (egglib.coalesce.ParamDict method)
(egglib.misc.Pool method)
(egglib.tools.Discretize method)
get_alt() (egglib.io.VcfParser method)
get_bed_file() (egglib.io.VcfParser method)
get_contig_index() (egglib.io.VcfParser method)
get_dEHH() (egglib.stats.EHH method)
get_dEHH_max() (egglib.stats.EHH method)
get_dEHH_mean() (egglib.stats.EHH method)
get_dEHHc() (egglib.stats.EHH method)
get_dEHHG() (egglib.stats.EHH method)
get_dEHHS() (egglib.stats.EHH method)
get_EHH() (egglib.stats.EHH method)
get_EHHc() (egglib.stats.EHH method)
get_EHHG() (egglib.stats.EHH method)
get_EHHS() (egglib.stats.EHH method)
get_fgenesh() (in module egglib.io)
get_filter() (egglib.io.VcfParser method)
get_format() (egglib.io.VcfParser method)
get_genotypes() (egglib.io.VcfParser method)
get_i() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
get_iEG() (egglib.stats.EHH method)
get_iES() (egglib.stats.EHH method)
get_IHH() (egglib.stats.EHH method)
get_IHHc() (egglib.stats.EHH method)
get_iHS() (egglib.stats.EHH method)
get_index() (egglib.io.VcfParser method)
get_info() (egglib.io.VcfParser method)
get_label() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
get_label_o() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
get_last_contig_index() (egglib.io.VcfParser method)
get_leaf() (egglib.Tree method)
get_meta() (egglib.io.VcfParser method)
get_name() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
get_name_o() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
get_o() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
get_outgroup() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
get_parent() (egglib.io.GFF3Feature method)
get_part() (egglib.io.GFF3Feature method)
get_position_index() (egglib.io.VcfParser method)
get_rEHH() (egglib.stats.EHH method)
get_sample() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
(egglib.io.VcfParser method)
get_seed() (egglib.tools.Random method)
get_sequence() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
(egglib.io.GenBankFeature method)
get_sequence_o() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
get_start() (egglib.io.GenBankFeature method)
get_stop() (egglib.io.GenBankFeature method)
get_structure() (egglib.stats.Structure method)
(in module egglib.stats)
get_type() (egglib.io.GenBankFeature method)
get_values() (egglib.coalesce.ParamDict method)
(egglib.coalesce.ParamMatrix method)
get_variant_index() (egglib.io.VcfParser method)
GFF3 (class in egglib.io)
GFF3Feature (class in egglib.io)
good (egglib.io._vcf.VcfWindow attribute)
(egglib.io.VcfParser attribute)
goto() (egglib.io.VcfParser method)
group (egglib.SampleView attribute)
group_mapping() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
GroupView (class in egglib)
GT (egglib.io.Variant attribute)
GT_phased (egglib.io.Variant attribute)
GT_ploidy (egglib.io.Variant attribute)
GT_vcf (egglib.io.Variant attribute)

H

haplotypes() (in module egglib.stats)
has_descendant() (egglib.Node method)
has_index (egglib.io.VcfParser attribute)
has_key() (egglib.coalesce.ParamDict method)
has_stop() (in module egglib.tools)

I

ID (egglib.io.GFF3Feature attribute)
(egglib.io.Variant attribute)
index (egglib.SampleView attribute)
index() (egglib.coalesce.ParamList method)
(egglib.coalesce.ParamMatrix method)
info (egglib.io.Variant attribute)
ingroup() (egglib.stats.Site method)
insert() (egglib.SequenceView method)
insert_columns() (egglib.Align method)
insert_sites() (egglib.Container method)
insert_sites_o() (egglib.Container method)
int2codon() (in module egglib.tools)
integer() (egglib.tools.Random method)
integer_32bit() (egglib.tools.Random method)
intersperse() (egglib.Align method)
is_child() (egglib.Node method)
is_circular (egglib.io.GFF3Feature attribute)
is_complement() (egglib.io.GenBankFeatureLocation method)
is_matrix (egglib._interface.DataBase attribute)
(egglib.Align attribute)
(egglib.Container attribute)
is_parent() (egglib.Node method)
is_range() (egglib.io.GenBankFeatureLocation method)
items() (egglib.coalesce.ParamDict method)
iter_codons() (egglib.tools.ReadingFrame method)
iter_exon_bounds() (egglib.tools.ReadingFrame method)
iter_leaves() (egglib.Tree method)
iter_NS() (egglib.stats.CodingDiversity method)
iter_outgroup() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
iter_S() (egglib.stats.CodingDiversity method)
iter_samples() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
iter_simul() (egglib.coalesce.Simulator method)
iter_stops() (in module egglib.tools)
iteritems() (egglib.coalesce.ParamDict method)
iterkeys() (egglib.coalesce.ParamDict method)
itervalues() (egglib.coalesce.ParamDict method)

K

keys() (egglib.coalesce.ParamDict method)

L

label (egglib.Node attribute)
last_variant() (egglib.io.VcfParser method)
lateralize() (egglib.Tree method)
leaves_down() (egglib.Node method)
leaves_up() (egglib.Node method)
left() (egglib.tools.Discretize method)
list_stats() (egglib.stats.ComputeStats method)
lo() (egglib.Container method)
load() (egglib.wrappers.path method)
load_align() (egglib.stats.ProbaMisoriented method)
load_distant() (egglib.stats.EHH method)
load_site() (egglib.stats.ProbaMisoriented method)
longest_orf() (in module egglib.tools)
ls (egglib.Align attribute)
(egglib.SampleView attribute)
ls() (egglib.Container method)

M

make_auxiliary() (egglib.stats.Structure method)
make_index() (egglib.io.VcfParser method)
make_structure() (egglib.stats.Structure method)
(in module egglib.stats)
map_descendants() (egglib.Tree method)
matrix_LD() (in module egglib.stats)
MAX (C++ member)
MAX_N_STIRLING (C++ member)
MAXCHAR (C++ member)
metadata (egglib.io.GFF3 attribute)
mget() (egglib.tools.Discretize method)
mid() (egglib.tools.Discretize method)
midroot() (egglib.Tree method)
MISSING (C++ member)
missing() (egglib.stats.Filter method)
MISSINGDATA (C++ member)
mk_align_NS() (egglib.stats.CodingDiversity method)
mk_align_S() (egglib.stats.CodingDiversity method)
mk_structure() (egglib.coalesce.ParamDict method)
motif_iter() (in module egglib.tools)
muscle() (in module egglib.wrappers)

N

n_index (egglib.io.VcfParser attribute)
name (egglib.io.GFF3Feature attribute)
(egglib.SampleView attribute)
(egglib.tools.BackalignError attribute)
name_mapping() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
names() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
names_outgroup() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
ncat (egglib.tools.Discretize attribute)
ndata (egglib.tools.Discretize attribute)
ndim (egglib.tools.Discretize attribute)
newick() (egglib.Node method)
(egglib.Tree method)
next() (egglib.io._vcf.VcfWindow method)
(egglib.io.VcfParser method)
(egglib.io.fasta_iter method)
nexus() (egglib.Align method)
ng (egglib._interface.DataBase attribute)
(egglib.Align attribute)
(egglib.Container attribute)
nieff() (egglib.stats.Freq method)
no (egglib._interface.DataBase attribute)
(egglib.Align attribute)
(egglib.Container attribute)
(egglib.stats.Site attribute)
(egglib.stats.Structure attribute)
Node (class in egglib)
normal() (egglib.tools.Random method)
notes (egglib.io.GFF3Feature attribute)
nout (egglib.coalesce.ParamDict attribute)
ns (egglib._interface.DataBase attribute)
(egglib.Align attribute)
(egglib.Container attribute)
(egglib.stats.Site attribute)
(egglib.stats.Structure attribute)
nsam (egglib.coalesce.ParamDict attribute)
(egglib.stats.EHH attribute)
nsam_core() (egglib.stats.EHH method)
nsam_hap() (egglib.stats.EHH method)
nseff() (egglib.stats.Freq method)
nskipped (egglib.tools.Discretize attribute)
num_alleles (egglib.io.Variant attribute)
(egglib.stats.Freq attribute)
(egglib.stats.Site attribute)
num_alt (egglib.io.VcfParser attribute)
num_alternate (egglib.io.Variant attribute)
num_children (egglib.Node attribute)
num_clust (egglib.stats.Structure attribute)
num_clusters (egglib.stats.Freq attribute)
num_codons (egglib.tools.ReadingFrame attribute)
num_codons_eff (egglib.stats.CodingDiversity attribute)
num_codons_stop (egglib.stats.CodingDiversity attribute)
num_codons_tot (egglib.stats.CodingDiversity attribute)
num_exon_bases (egglib.tools.ReadingFrame attribute)
num_exons (egglib.tools.ReadingFrame attribute)
num_filter (egglib.io.VcfParser attribute)
num_format (egglib.io.VcfParser attribute)
num_fragments (egglib.io.GFF3Feature attribute)
num_full_codons (egglib.tools.ReadingFrame attribute)
num_genotypes (egglib.stats.Freq attribute)
num_haplotypes (egglib.stats.EHH attribute)
num_indiv_ingroup (egglib.stats.Structure attribute)
num_indiv_outgroup (egglib.stats.Structure attribute)
num_info (egglib.io.VcfParser attribute)
num_ingroup (egglib.stats.Site attribute)
num_leaves (egglib.Tree attribute)
num_meta (egglib.io.VcfParser attribute)
num_missing (egglib.stats.Site attribute)
num_missing_ingroup (egglib.stats.Site attribute)
num_missing_outgroup (egglib.stats.Site attribute)
num_multiple_alleles (egglib.stats.CodingDiversity attribute)
num_multiple_hits (egglib.stats.CodingDiversity attribute)
num_needed_bases (egglib.tools.ReadingFrame attribute)
num_nodes (egglib.Tree attribute)
num_outgroup (egglib.stats.Site attribute)
num_parents (egglib.io.GFF3Feature attribute)
num_parts (egglib.io.GFF3Feature attribute)
num_pol_NS (egglib.stats.CodingDiversity attribute)
num_pol_S (egglib.stats.CodingDiversity attribute)
num_pol_single (egglib.stats.CodingDiversity attribute)
num_pop (egglib.stats.Structure attribute)
num_populations (egglib.stats.Freq attribute)
num_samples (egglib.io.Variant attribute)
(egglib.io.VcfParser attribute)
num_sites (egglib.io._vcf.VcfWindow attribute)
num_sites() (egglib.stats.ParalogPi method)
num_sites_NS (egglib.stats.CodingDiversity attribute)
num_sites_S (egglib.stats.CodingDiversity attribute)
NUM_STIRLING (C++ member)
num_top_features (egglib.io.GFF3 attribute)
num_tot_bases (egglib.tools.ReadingFrame attribute)
num_tot_features (egglib.io.GFF3 attribute)
number_of_features() (egglib.io.GenBank method)

O

ontology_terms (egglib.io.GFF3Feature attribute)
orf_iter() (in module egglib.tools)
OUTGROUP (C++ member)
outgroup (egglib.GroupView attribute)
(egglib.SampleView attribute)
outgroup() (egglib.stats.Site method)

P

pairwise_LD() (in module egglib.stats)
paralog_pi() (in module egglib.stats)
ParalogPi (class in egglib.stats)
ParamDict (class in egglib.coalesce)
ParamList (class in egglib.coalesce)
ParamMatrix (class in egglib.coalesce)
params (egglib.coalesce.Simulator attribute)
parent (egglib.Node attribute)
(egglib.SampleView attribute)
parent_branch (egglib.Node attribute)
parse() (egglib.io.GenBankFeature method)
phase (egglib.io.GFF3Feature attribute)
phylip() (egglib.Align method)
phyml() (egglib.Align method)
(in module egglib.wrappers)
Pib() (egglib.stats.ParalogPi method)
Piw() (egglib.stats.ParalogPi method)
ploidy (egglib.stats.Freq attribute)
(egglib.stats.Site attribute)
(egglib.stats.Structure attribute)
pM (egglib.stats.ProbaMisoriented attribute)
poisson() (egglib.tools.Random method)
Pool (class in egglib.misc)
position (egglib.io.Variant attribute)
positions (egglib.io.GFF3Feature attribute)
ProbaMisoriented (class in egglib.stats)
process() (egglib.stats.CodingDiversity method)
(egglib.tools.Discretize method)
(egglib.tools.ReadingFrame method)
process_align() (egglib.stats.ComputeStats method)
(egglib.stats.ParalogPi method)
(egglib.stats.Site method)
process_freq() (egglib.stats.ComputeStats method)
process_list() (egglib.stats.Freq method)
(egglib.stats.Site method)
process_site() (egglib.stats.ComputeStats method)
(egglib.stats.Freq method)
(egglib.stats.ParalogPi method)
process_sites() (egglib.stats.ComputeStats method)
process_vcf() (egglib.stats.Freq method)
(egglib.stats.Site method)
put() (egglib.misc.Pool method)

Q

qualifiers() (egglib.io.GenBankFeature method)
quality (egglib.io.Variant attribute)

R

Random (class in egglib.tools)
random_missing() (egglib.Align method)
rc() (egglib.io.GenBank method)
(egglib.io.GenBankFeature method)
(egglib.io.GenBankFeatureLocation method)
(in module egglib.tools)
read_index() (egglib.io.VcfParser method)
read_line() (egglib.io.VcfParser method)
ReadingFrame (class in egglib.tools)
regex() (in module egglib.tools)
remove_duplicates() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
remove_node() (egglib.Tree method)
rename() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
replace() (egglib.coalesce.EventList method)
req_no (egglib.stats.Structure attribute)
req_ns (egglib.stats.Structure attribute)
reserve() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
reset() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
(egglib.stats.ComputeStats method)
(egglib.stats.ProbaMisoriented method)
(egglib.stats.Site method)
(egglib.tools.Discretize method)
results() (egglib.stats.ComputeStats method)
rewind() (egglib.io.VcfParser method)
right() (egglib.tools.Discretize method)
rng() (egglib.stats.Filter method)
root() (egglib.Tree method)

S

S (egglib.stats.ProbaMisoriented attribute)
samples (egglib.io.Variant attribute)
SampleView (class in egglib)
save() (egglib.wrappers.path method)
score (egglib.io.GFF3Feature attribute)
seqid (egglib.io.GFF3 attribute)
(egglib.io.GFF3Feature attribute)
sequence (egglib.io.GenBank attribute)
(egglib.SampleView attribute)
SequenceView (class in egglib)
set_branch_to() (egglib.Node method)
set_complement() (egglib.io.GenBankFeatureLocation method)
set_core() (egglib.stats.EHH method)
set_forward() (egglib.io.GenBankFeatureLocation method)
set_i() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
set_label() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
set_label_o() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
set_migr() (egglib.coalesce.ParamDict method)
set_name() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
set_name_o() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
set_o() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
set_outgroup() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
set_sample() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
set_seed() (egglib.tools.Random method)
set_sequence() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
set_sequence_o() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
setup() (egglib.stats.ParalogPi method)
shift() (egglib.io.GenBankFeature method)
(egglib.io.GenBankFeatureLocation method)
shuffle() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
siblings() (egglib.Node method)
simul() (egglib.coalesce.Simulator method)
Simulator (class in egglib.coalesce)
Site (class in egglib.stats)
site_from_align() (in module egglib.stats)
site_from_list() (in module egglib.stats)
site_from_vcf() (in module egglib.stats)
size() (egglib.io._vcf.VcfWindow method)
slider() (egglib.Align method)
(egglib.io.VcfParser method)
source (egglib.io.GFF3Feature attribute)
start (egglib.io.GFF3Feature attribute)
start_position (egglib.io._vcf.VcfWindow attribute)
STIRLING_TABLE (C++ member)
string() (egglib.SequenceView method)
strip() (egglib.SequenceView method)
Structure (class in egglib.stats)
subgroup() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
subset() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
summary() (egglib.coalesce.ParamDict method)

T

target (egglib.io.GFF3Feature attribute)
TempFile (class in egglib.misc)
TiTv (egglib.stats.ProbaMisoriented attribute)
to_fasta() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
to_lower() (egglib.SequenceView method)
to_ms() (in module egglib.io)
to_outgroup() (egglib._interface.DataBase method)
(egglib.Align method)
(egglib.Container method)
to_upper() (egglib.SequenceView method)
total_length() (egglib.Tree method)
trailing_stops() (in module egglib.tools)
translate() (in module egglib.tools)
translate_align() (egglib.tools.Translator method)
translate_codon() (egglib.tools.Translator method)
translate_container() (egglib.tools.Translator method)
translate_sequence() (egglib.tools.Translator method)
Translator (class in egglib.tools)
Tree (class in egglib)
type (egglib.io.GFF3Feature attribute)
types (egglib.io.GFF3 attribute)

U

UNDEF (C++ member)
ungap() (in module egglib.tools)
uniform() (egglib.tools.Random method)
uniform_53bit() (egglib.tools.Random method)
uniform_closed() (egglib.tools.Random method)
uniform_open() (egglib.tools.Random method)
UNKNOWN (C++ member)
unread() (egglib.io.VcfParser method)
unroot() (egglib.Tree method)
update() (egglib.coalesce.EventList method)
(egglib.coalesce.ParamDict method)
(egglib.io.GenBankFeature method)

V

values() (egglib.coalesce.ParamDict method)
Variant (class in egglib.io)
VcfParser (class in egglib.io)
VcfWindow (class in egglib.io._vcf)

W

write() (egglib.io.GenBank method)
write_stream() (egglib.io.GenBank method)