Index

A

AA (egglib.io.VcfVariant property) AC (egglib.io.VcfVariant property) accession (egglib.wrappers.BlastHit property) 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_exploitable() (egglib.Alphabet method) add_feature() (egglib.io.GenBank method) add_label() (egglib.Align method) (egglib.Container method) add_missing() (egglib.Alphabet method) add_node() (egglib.Tree method) add_qualifier() (egglib.io.GenBankFeature method) add_sample() (egglib.Align method) (egglib.Container method) add_samples() (egglib.Align method) (egglib.Container method) add_single_base() (egglib.io.GenBankFeatureLocation method) add_stats() (egglib.stats.ComputeStats method) AF (egglib.io.VcfVariant property) Align (class in egglib) align (egglib.coalesce.Simulator property)

align_len (egglib.wrappers.BlastHsp property) alignment (egglib.tools.BackalignError property) all_parts (egglib.io.Gff3Feature property) all_stats() (egglib.stats.ComputeStats method) allele() (egglib.Freq method) alleles (egglib.io.VcfVariant property) Alphabet (class in egglib) alphabet (egglib.Align property) (egglib.Container property) (egglib.Site property) alt_type_breakend (egglib.io.VcfVariant attribute) alt_type_default (egglib.io.VcfVariant attribute) alt_type_referred (egglib.io.VcfVariant attribute) alternate_types (egglib.io.VcfVariant property) AN (egglib.io.VcfVariant property) append() (egglib.io.BED method) (egglib.LabelView method) (egglib.Site method) as_dict() (egglib.Structure method) as_list() (egglib.Site method) as_order() (egglib.io.GenBankFeatureLocation method) as_range() (egglib.io.GenBankFeatureLocation method) attribute_ontology (egglib.io.GFF3 property) attributes (egglib.io.Gff3Feature property) autodetect() (egglib.wrappers.paths method)

B

backalign() (in module egglib.tools) BackalignError (class in egglib.tools) base (egglib.Tree property) BED (class in egglib.io) bed_slider() (egglib.io.VcfParser method) bernoulli() (in module egglib.random) binary (in module egglib.alphabets) binomial() (in module egglib.random) bit_score (egglib.wrappers.BlastHsp property) BlastHit (class in egglib.wrappers) BlastHsp (class in egglib.wrappers) blastn() (in module egglib.wrappers)

blastn_short() (in module egglib.wrappers) BlastOutput (class in egglib.wrappers) blastp() (in module egglib.wrappers) blastp_fast() (in module egglib.wrappers) blastp_short() (in module egglib.wrappers) BlastQueryHits (class in egglib.wrappers) blastx() (in module egglib.wrappers) blastx_fast() (in module egglib.wrappers) boolean() (in module egglib.random) bounds (egglib.io.VcfWindow property) branch_to() (egglib.Node method) breadth_iter() (egglib.Tree method)

C

case_insensitive (egglib.Alphabet property) child() (egglib.Node method) children() (egglib.Node method) chromosome (egglib.io.VcfVariant property) (egglib.io.VcfWindow property) clean_branch_lengths() (egglib.Tree method) clean_internal_labels() (egglib.Tree method) clear() (egglib.Align method) (egglib.coalesce.EventList method) (egglib.Container method) clear_stats() (egglib.stats.ComputeStats method) close() (egglib.io.VcfParser 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) codons (in module egglib.alphabets)

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) configure() (egglib.stats.ComputeStats method) consensus() (egglib.Align method) Container (class in egglib) copy() (egglib.coalesce.ParamDict method) (egglib.io.GenBankFeature method) (egglib.io.GenBankFeatureLocation method) (egglib.Tree method) count() (egglib.coalesce.ParamList method) (egglib.coalesce.ParamMatrix method) create() (egglib.Align class method) (egglib.Container class method) cur_haplotypes (egglib.stats.EHH property) currline (egglib.io.VcfParser property)

D

D (egglib.stats.ProbaMisoriented property) db (egglib.wrappers.BlastOutput property) db_len (egglib.wrappers.BlastQueryHits property) db_num (egglib.wrappers.BlastQueryHits property) dc_megablast() (in module egglib.wrappers) del_columns() (egglib.Align method) del_sample() (egglib.Align method) (egglib.Container method)

del_sites() (egglib.Container method) depth_iter() (egglib.Tree method) derivers (egglib.io.Gff3Feature property) descendants (egglib.io.Gff3Feature property) descr (egglib.wrappers.BlastHit property) disable_trans_matrix() (egglib.coalesce.ParamDict method) DNA (in module egglib.alphabets) done_EHH() (egglib.stats.EHH method) done_EHHc() (egglib.stats.EHH method)

E

eff_space (egglib.wrappers.BlastQueryHits property) EHH (class in egglib.stats) encode (class in egglib) encode() (egglib.Align method) (egglib.Container method) end (egglib.io.Gff3Feature property) equalize() (egglib.Container method) evalue (egglib.wrappers.BlastHsp property)

EventList (class in egglib.coalesce) exon_index() (egglib.tools.ReadingFrame method) exponential() (in module egglib.random) extend() (egglib.io.BED method) (egglib.Site method) extract() (egglib.Align method) (egglib.io.GenBank method) (egglib.Tree method)

F

failed_tests (egglib.io.VcfVariant property) fasta() (egglib.Align method) (egglib.Container method) fasta_iter (class in egglib.io) feature_ontology (egglib.io.GFF3 property) file_format (egglib.io.VcfParser property) (egglib.io.VcfStringParser property) filter() (egglib.Align method) find() (egglib.Align method) (egglib.Container method) (egglib.SequenceView method) find_clade() (egglib.Tree method) find_motif() (egglib.Align method) (egglib.Container method) FIRST (in module egglib.io) fix_ends() (egglib.Align method) format() (egglib.io.GenBank method) (egglib.io.GenBankFeature method) (egglib.io.GenBankFeatureLocation method) format_fields (egglib.io.VcfVariant property) Freq (class in egglib) freq_allele() (egglib.Freq method)

freq_from_list() (in module egglib) freq_from_site() (in module egglib) freq_from_vcf() (in module egglib) freq_genotype() (egglib.Freq method) frequency_nodes() (egglib.Tree method) from_align() (egglib.Site method) from_clustal() (in module egglib.io) from_dict() (egglib.Structure method) from_fasta() (in module egglib.io) from_fasta_string() (in module egglib.io) from_genalys() (in module egglib.io) from_genepop() (in module egglib.io) from_iterable() (egglib.Structure method) from_labels() (egglib.Structure method) from_list() (egglib.Freq method) (egglib.Site method) from_samplesizes() (egglib.Structure method) from_site() (egglib.Freq method) from_staden() (in module egglib.io) from_string() (egglib.io.GFF3 class method) from_vcf() (egglib.Freq method) (egglib.Site method)

G

gaps (egglib.wrappers.BlastHsp property) GenBank (class in egglib.io) GenBankFeature (class in egglib.io) GenBankFeatureLocation (class in egglib.io) genepop (in module egglib.alphabets) genome_build (egglib.io.GFF3 property) genotype() (egglib.Freq method) geometric() (in module egglib.random) get() (egglib.Align method) (egglib.coalesce.ParamDict method) (egglib.Container method) get_alleles() (egglib.Alphabet method) (egglib.io.VCF method) get_alt() (egglib.io.VcfParser method) (egglib.io.VcfStringParser method) get_alternate() (egglib.io.VCF method) get_chrom() (egglib.io.VCF method) get_clusters() (egglib.Structure method) get_code() (egglib.Alphabet 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_errors() (egglib.io.VCF method) get_fgenesh() (in module egglib.io) get_filter() (egglib.io.VCF method) (egglib.io.VcfParser method) (egglib.io.VcfStringParser method) get_format() (egglib.io.VCF method) (egglib.io.VcfParser method) (egglib.io.VcfStringParser method) get_formats() (egglib.io.VCF method) get_genotypes() (egglib.io.VCF method) (egglib.io.VcfParser method) (egglib.io.VcfStringParser method) get_hit() (egglib.wrappers.BlastQueryHits method) get_hsp() (egglib.wrappers.BlastHit method) get_id() (egglib.io.VCF 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_info() (egglib.io.VCF method) (egglib.io.VcfParser method) (egglib.io.VcfStringParser method) get_infos() (egglib.io.VCF method) get_label() (egglib.Align method) (egglib.Container method) get_leaf() (egglib.Tree method) get_meta() (egglib.io.VcfParser method) (egglib.io.VcfStringParser method) get_name() (egglib.Align method) (egglib.Container method) get_phased() (egglib.io.VCF method) get_populations() (egglib.Structure method) get_pos() (egglib.io.VCF method) get_quality() (egglib.io.VCF method) get_query() (egglib.wrappers.BlastOutput method) get_reference() (egglib.io.VCF method) get_rEHH() (egglib.stats.EHH method) get_sample() (egglib.Align method) (egglib.Container method) (egglib.io.VCF method) (egglib.io.VcfParser method) (egglib.io.VcfStringParser method) get_samples() (egglib.io.VCF method) (egglib.Structure method) get_seed() (in module egglib.random) get_sequence() (egglib.Align method) (egglib.Container method) (egglib.io.GenBankFeature method) get_start() (egglib.io.GenBankFeature method) get_stop() (egglib.io.GenBankFeature method) get_type() (egglib.io.GenBankFeature method) get_types() (egglib.io.VCF method) get_value() (egglib.Alphabet method) get_values() (egglib.coalesce.ParamDict method) (egglib.coalesce.ParamMatrix method) get_variant() (egglib.io.VcfParser method) (egglib.io.VcfStringParser method) GFF3 (class in egglib.io) Gff3Feature (class in egglib.io) GL (egglib.io.VcfVariant property) good (egglib.io.VcfParser property) (egglib.io.VcfSlidingWindow property) goto() (egglib.io.VCF method) (egglib.io.VcfParser method) group_mapping() (egglib.Align method) (egglib.Container method) GT (egglib.io.VcfVariant property) GT_phased (egglib.io.VcfVariant property) GT_vcf (egglib.io.VcfVariant property)

H

H (egglib.wrappers.BlastQueryHits property) haplotypes_from_align() (in module egglib.stats) haplotypes_from_sites() (in module egglib.stats) has_descendant() (egglib.Node method) has_index (egglib.io.VCF attribute) (egglib.io.VcfParser property)

has_key() (egglib.coalesce.ParamDict method) has_stop() (in module egglib.tools) hit_frame (egglib.wrappers.BlastHsp property) hit_start (egglib.wrappers.BlastHsp property) hit_stop (egglib.wrappers.BlastHsp property) hseq (egglib.wrappers.BlastHsp property) hsp_len (egglib.wrappers.BlastQueryHits property)

I

ID (egglib.io.Gff3Feature property) (egglib.io.VcfVariant property) id (egglib.wrappers.BlastHit property) identity (egglib.wrappers.BlastHsp property) index (egglib.SampleView property) index() (egglib.coalesce.ParamList method) (egglib.coalesce.ParamMatrix method) index_vcf() (in module egglib.io) info (egglib.io.VcfVariant property) insert() (egglib.SequenceView method) insert_columns() (egglib.Align method) insert_sites() (egglib.Container method) integer() (in module egglib.random) integer_32bit() (in module egglib.random) intersperse() (egglib.Align method) is_child() (egglib.Node method) is_complement() (egglib.io.GenBankFeatureLocation method) is_matrix (egglib.Align property) (egglib.Container property)

is_parent() (egglib.Node method) is_range() (egglib.io.GenBankFeatureLocation method) is_snp() (egglib.io.VCF method) items() (egglib.coalesce.ParamDict method) iter_codons() (egglib.tools.ReadingFrame method) iter_exon_bounds() (egglib.tools.ReadingFrame method) iter_features() (egglib.io.GFF3 method) iter_hits() (egglib.wrappers.BlastOutput method) (egglib.wrappers.BlastQueryHits method) iter_hsp() (egglib.wrappers.BlastHit method) (egglib.wrappers.BlastOutput method) (egglib.wrappers.BlastQueryHits method) iter_leaves() (egglib.Tree method) iter_queries() (egglib.wrappers.BlastOutput method) iter_simul() (egglib.coalesce.Simulator method) iter_sites() (egglib.Align method) iter_stops() (in module egglib.tools)

K

K (egglib.wrappers.BlastQueryHits property)

keys() (egglib.coalesce.ParamDict method)

L

L (egglib.wrappers.BlastQueryHits property) label (egglib.Node property) labels (egglib.SampleView property) LabelView (class in egglib) LAST (in module egglib.io) lateralize() (egglib.Tree method) leaves_down() (egglib.Node method) leaves_up() (egglib.Node method) len (egglib.wrappers.BlastHit property) list_seqid (egglib.io.GFF3 property) list_stats() (egglib.stats.ComputeStats method) load() (egglib.wrappers.path method) load_align() (egglib.stats.ProbaMisoriented method)

load_distant() (egglib.stats.EHH method) load_index() (egglib.io.VcfParser method) load_site() (egglib.stats.ProbaMisoriented method) lock() (egglib.Alphabet method) locked (egglib.Alphabet property) longest_orf() (in module egglib.tools) lower() (egglib.Align method) (egglib.Container method) (egglib.SequenceView method) ls (egglib.Align property) (egglib.SampleView property) ls() (egglib.Container method) lstrip() (egglib.SequenceView method)

M

make_auxiliary() (egglib.Structure method) make_sorted_auxiliary() (egglib.Structure method) make_vcf_index() (in module egglib.io) makeblastdb() (in module egglib.wrappers) map_descendants() (egglib.Tree method) matrix_LD() (in module egglib.stats) megablast() (in module egglib.wrappers)

midline (egglib.wrappers.BlastHsp property) midroot() (egglib.Tree method) mk_structure() (egglib.coalesce.ParamDict method) motif_iter() (in module egglib.tools) muscle() (in module egglib.wrappers) muscle3() (in module egglib.wrappers) muscle5() (in module egglib.wrappers)

N

name (egglib.Alphabet property) (egglib.SampleView property) (egglib.tools.BackalignError property) name_mapping() (egglib.Align method) (egglib.Container method) names() (egglib.Align method) (egglib.Container method) newick() (egglib.Node method) (egglib.Tree method) nexus() (egglib.Align method) nieff() (egglib.Freq method) nj() (in module egglib.wrappers) no (egglib.Structure property) Node (class in egglib) normal() (in module egglib.random) normal_bounded() (in module egglib.random) ns (egglib.Align property) (egglib.Container property) (egglib.Site property) (egglib.Structure property) nsam (egglib.stats.EHH property) nsam_core() (egglib.stats.EHH method) nsam_hap() (egglib.stats.EHH method) nseff() (egglib.Freq method) num (egglib.wrappers.BlastHit property) (egglib.wrappers.BlastHsp property) (egglib.wrappers.BlastQueryHits property) num_alleles (egglib.Alphabet property) (egglib.Freq property) (egglib.io.VcfVariant property) num_alt (egglib.io.VcfParser property) (egglib.io.VcfStringParser property) num_alternate (egglib.io.VcfVariant property) num_children (egglib.Node property) num_clust (egglib.Structure property) num_clusters (egglib.Freq property) num_codons (egglib.tools.ReadingFrame property) num_codons_eff (egglib.stats.CodingDiversity property) num_codons_stop (egglib.stats.CodingDiversity property) num_codons_tot (egglib.stats.CodingDiversity property) num_exon_bases (egglib.tools.ReadingFrame property) num_exons (egglib.tools.ReadingFrame property) num_exploitable (egglib.Alphabet property) num_filter (egglib.io.VcfParser property) (egglib.io.VcfStringParser property)

num_format (egglib.io.VcfParser property) (egglib.io.VcfStringParser property) num_genotypes (egglib.Freq property) (egglib.io.VcfVariant property) num_haplotypes (egglib.stats.EHH property) num_hits (egglib.wrappers.BlastOutput property) (egglib.wrappers.BlastQueryHits property) num_hsp (egglib.wrappers.BlastHit property) (egglib.wrappers.BlastOutput property) (egglib.wrappers.BlastQueryHits property) num_index (egglib.io.VcfParser property) num_indiv_ingroup (egglib.Structure property) num_indiv_outgroup (egglib.Structure property) num_info (egglib.io.VcfParser property) (egglib.io.VcfStringParser property) num_leaves (egglib.Tree property) num_meta (egglib.io.VcfParser property) (egglib.io.VcfStringParser property) num_missing (egglib.Alphabet property) (egglib.Site property) num_multiple_alleles (egglib.stats.CodingDiversity property) num_multiple_hits (egglib.stats.CodingDiversity property) num_needed_bases (egglib.tools.ReadingFrame property) num_nodes (egglib.Tree property) num_pol_NS (egglib.stats.CodingDiversity property) num_pol_S (egglib.stats.CodingDiversity property) num_pol_single (egglib.stats.CodingDiversity property) num_pop (egglib.Structure property) num_populations (egglib.Freq property) num_queries (egglib.wrappers.BlastOutput property) num_samples (egglib.io.VCF attribute) (egglib.io.VcfParser property) (egglib.io.VcfStringParser property) (egglib.io.VcfVariant property) num_seqid (egglib.io.GFF3 property) num_sites (egglib.io.VcfWindow property) num_sites() (egglib.stats.ParalogPi method) num_sites_NS (egglib.stats.CodingDiversity property) num_sites_S (egglib.stats.CodingDiversity property) num_top_features (egglib.io.GFF3 property) num_tot_bases (egglib.tools.ReadingFrame property) num_tot_features (egglib.io.GFF3 property) number_of_features() (egglib.io.GenBank method)

O

orf_iter() (in module egglib.tools)

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 property) (egglib.wrappers.BlastOutput property) parent (egglib.Node property) (egglib.SampleView property) parent_branch (egglib.Node property) parents (egglib.io.Gff3Feature property) parse() (egglib.io.GenBankFeature method) phylip() (egglib.Align method) phyml() (egglib.Align method) (in module egglib.wrappers) Pib() (egglib.stats.ParalogPi method) Piw() (egglib.stats.ParalogPi method) PL (egglib.io.VcfVariant property) ploidy (egglib.Freq property) (egglib.io.VcfVariant property) (egglib.Structure property)

pM (egglib.stats.ProbaMisoriented property) poisson() (in module egglib.random) position (egglib.io.VcfVariant property) (egglib.Site property) positions_NS (egglib.stats.CodingDiversity property) positions_S (egglib.stats.CodingDiversity property) positive (egglib.wrappers.BlastHsp property) positive_infinite (in module egglib.alphabets) ProbaMisoriented (class in egglib.stats) process() (egglib.stats.CodingDiversity method) (egglib.tools.ReadingFrame method) process_align() (egglib.stats.ComputeStats method) (egglib.stats.ParalogPi method) process_freq() (egglib.stats.ComputeStats method) process_site() (egglib.stats.ComputeStats method) (egglib.stats.ParalogPi method) process_sites() (egglib.stats.ComputeStats method) program (egglib.wrappers.BlastOutput property) protein (in module egglib.alphabets)

Q

qseq (egglib.wrappers.BlastHsp property) qualifiers() (egglib.io.GenBankFeature method) quality (egglib.io.VcfVariant property) query_def (egglib.wrappers.BlastOutput property) (egglib.wrappers.BlastQueryHits property) query_frame (egglib.wrappers.BlastHsp property)

query_ID (egglib.wrappers.BlastOutput property) (egglib.wrappers.BlastQueryHits property) query_len (egglib.wrappers.BlastOutput property) (egglib.wrappers.BlastQueryHits property) query_start (egglib.wrappers.BlastHsp property) query_stop (egglib.wrappers.BlastHsp property)

R

random_missing() (egglib.Align method) rc() (egglib.io.GenBank method) (egglib.io.GenBankFeature method) (egglib.io.GenBankFeatureLocation method) (in module egglib.tools) read() (egglib.io.VCF method) ReadingFrame (class in egglib.tools) readline() (egglib.io.VcfParser method) (egglib.io.VcfStringParser method) reference (egglib.wrappers.BlastOutput property) regex() (in module egglib.tools) regions (egglib.io.GFF3 property) remove_duplicates() (egglib.Align method) (egglib.Container method) remove_node() (egglib.Tree method)

rename() (egglib.Align method) (egglib.Container method) replace() (egglib.coalesce.EventList method) req_ns (egglib.Structure property) reserve() (egglib.Align method) (egglib.Container method) reset() (egglib.Align method) (egglib.Container method) (egglib.Site method) (egglib.stats.ComputeStats method) (egglib.stats.ProbaMisoriented method) results() (egglib.stats.ComputeStats method) rewind() (egglib.io.VcfParser method) root() (egglib.Tree method) rstrip() (egglib.SequenceView method)

S

S (egglib.stats.ProbaMisoriented property) samples (egglib.io.VcfVariant property) SampleView (class in egglib) save() (egglib.wrappers.path method) score (egglib.io.Gff3Feature property) segments (egglib.io.Gff3Feature property) seqid (egglib.io.Gff3Feature property) sequence (egglib.io.GenBank property) (egglib.SampleView property) sequences (egglib.io.GFF3 property) SequenceView (class in egglib) set() (egglib.Align method) (egglib.Container method) 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_label() (egglib.Align method) (egglib.Container method) set_migr() (egglib.coalesce.ParamDict method) set_name() (egglib.Align method) (egglib.Container method) set_sample() (egglib.Align method) (egglib.Container method) set_seed() (in module egglib.random) set_sequence() (egglib.Align method) (egglib.Container method) set_structure() (egglib.stats.ComputeStats method) setup() (egglib.stats.ParalogPi method)

shift() (egglib.io.GenBankFeature method) (egglib.io.GenBankFeatureLocation method) shuffle() (egglib.Structure method) siblings() (egglib.Node method) simul() (egglib.coalesce.Simulator method) Simulator (class in egglib.coalesce) Site (class in egglib) site_from_align() (in module egglib) site_from_list() (in module egglib) site_from_vcf() (in module egglib) sites_NS (egglib.stats.CodingDiversity property) sites_S (egglib.stats.CodingDiversity property) slider() (egglib.Align method) (egglib.io.VcfParser method) source (egglib.io.Gff3Feature property) source_ontology (egglib.io.GFF3 property) species (egglib.io.GFF3 property) start (egglib.io.Gff3Feature property) strand (egglib.io.Gff3Feature property) string() (egglib.SequenceView method) strip() (egglib.SequenceView method) struct_from_dict() (in module egglib) struct_from_iterable() (in module egglib) struct_from_labels() (in module egglib) struct_from_samplesizes() (in module egglib) Structure (class in egglib) subset() (egglib.Align method) (egglib.Container method) (egglib.Structure method) summary() (egglib.coalesce.ParamDict method)

T

tblastn() (in module egglib.wrappers) tblastn_fast() (in module egglib.wrappers) tblastx() (in module egglib.wrappers) TiTv (egglib.stats.ProbaMisoriented property) to_bases() (egglib.Align method) (egglib.Container method) (in module egglib.tools) to_codons() (egglib.Align method) (egglib.Container method) (in module egglib.tools) to_ms() (in module egglib.io)

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.Alphabet property) (egglib.io.Gff3Feature property)

U

ungap() (in module egglib.tools) ungap_all() (in module egglib.tools) uniform() (in module egglib.random) uniform_53bit() (in module egglib.random) uniform_closed() (in module egglib.random) uniform_open() (in module egglib.random) unread() (egglib.io.VcfParser method)

unroot() (egglib.Tree method) update() (egglib.coalesce.EventList method) (egglib.coalesce.ParamDict method) (egglib.io.GenBankFeature method) upper() (egglib.Align method) (egglib.Container method) (egglib.SequenceView method)

V

values() (egglib.coalesce.ParamDict method) VCF (class in egglib.io) VcfParser (class in egglib.io) VcfSlidingWindow (class in egglib.io)

VcfStringParser (class in egglib.io) VcfVariant (class in egglib.io) VcfWindow (class in egglib.io) version (egglib.io.GFF3 property) (egglib.wrappers.BlastOutput property)

W

write() (egglib.io.GenBank method)

write_stream() (egglib.io.GenBank method)