Docs
2020.6.30a
Install
Gallery
Sections
Page
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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L
|
M
|
N
|
O
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P
|
Q
|
R
|
S
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T
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U
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V
|
W
A
add_annotation() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
add_feature() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
add_from_ref_aln() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
add_seqs() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
Alignment (class in cogent3.core.alignment)
alignment_quality() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
alphabet (cogent3.core.alignment.ArrayAlignment attribute)
ancestors() (cogent3.core.tree.PhyloNode method)
annotate_from_gff() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
annotate_matches_to() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
annotations (cogent3.core.alignment.Alignment attribute)
(cogent3.core.sequence.DnaSequence attribute)
(cogent3.core.sequence.ProteinSequence attribute)
(cogent3.core.sequence.RnaSequence attribute)
append() (cogent3.core.tree.PhyloNode method)
appended() (cogent3.util.table.Table method)
apply_pssm() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
array() (cogent3.util.table.Table property)
ArrayAlignment (class in cogent3.core.alignment)
ascii_art() (cogent3.core.tree.PhyloNode method)
attach_annotations() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
B
balanced() (cogent3.core.tree.PhyloNode method)
bifurcating() (cogent3.core.tree.PhyloNode method)
C
can_match() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
can_mismatch() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
can_mispair() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
can_pair() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
child_groups() (cogent3.core.tree.PhyloNode method)
clear_annotations() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
codon_alphabet() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
coevolution() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
cogent.app
cogent.db.ensembl
cogent.db.eutils
cogent.maths.unifrac
cogent.motif
cogent.seqsim
cogent.struct
cogent3.util.misc
compare_by_names() (cogent3.core.tree.PhyloNode method)
compare_by_subsets() (cogent3.core.tree.PhyloNode method)
compare_by_tip_distances() (cogent3.core.tree.PhyloNode method)
compare_name() (cogent3.core.tree.PhyloNode method)
complement() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
copy() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
(cogent3.core.tree.PhyloNode method)
copy_annotations() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
copy_recursive() (cogent3.core.tree.PhyloNode method)
copy_topology() (cogent3.core.tree.PhyloNode method)
count() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
(cogent3.util.table.Table method)
count_degenerate() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
count_gaps() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
count_gaps_per_pos() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
count_gaps_per_seq() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
count_unique() (cogent3.util.table.Table method)
counts() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
counts_per_pos() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
counts_per_seq() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
cross_join() (cogent3.util.table.Table method)
D
deepcopy() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.tree.PhyloNode method)
default_gap (cogent3.core.alignment.Alignment attribute)
(cogent3.core.alignment.ArrayAlignment attribute)
degap() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
descendant_array() (cogent3.core.tree.PhyloNode method)
detach_annotations() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
diff() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
disambiguate() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
distance() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
(cogent3.core.tree.PhyloNode method)
distance_matrix() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
distinct_values() (cogent3.util.table.Table method)
DnaSequence (class in cogent3.core.sequence)
dotplot() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
E
entropy_per_pos() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
entropy_per_seq() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
extend() (cogent3.core.tree.PhyloNode method)
F
filtered() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.util.table.Table method)
filtered_by_column() (cogent3.util.table.Table method)
first_degenerate() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
first_gap() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
first_invalid() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
first_non_strict() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
format() (cogent3.util.table.Table property)
format_column() (cogent3.util.table.Table method)
frac_diff() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
frac_diff_gaps() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
frac_diff_non_gaps() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
frac_same() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
frac_same_gaps() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
frac_same_non_gaps() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
frac_similar() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
G
gap_chars (cogent3.core.alignment.Alignment attribute)
(cogent3.core.alignment.ArrayAlignment attribute)
gap_indices() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
gap_maps() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
gap_vector() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
gapped_by_map() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
gapped_by_map_motif_iter() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
gapped_by_map_segment_iter() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
get_ambiguous_positions() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
get_annotations_from_any_seq() (cogent3.core.alignment.Alignment method)
get_annotations_from_seq() (cogent3.core.alignment.Alignment method)
get_annotations_matching() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
get_by_annotation() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
get_by_seq_annotation() (cogent3.core.alignment.Alignment method)
get_color_scheme() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
get_colour_scheme() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
get_columns() (cogent3.util.table.Table method)
get_connecting_edges() (cogent3.core.tree.PhyloNode method)
get_connecting_node() (cogent3.core.tree.PhyloNode method)
get_degapped_relative_to() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
get_distances() (cogent3.core.tree.PhyloNode method)
get_drawable() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
get_drawables() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
get_edge_names() (cogent3.core.tree.PhyloNode method)
get_edge_vector() (cogent3.core.tree.PhyloNode method)
get_figure() (cogent3.core.tree.PhyloNode method)
get_gap_array() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
get_gapped_seq() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
get_identical_sets() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
get_in_motif_size() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
get_lengths() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
get_max_tip_tip_distance() (cogent3.core.tree.PhyloNode method)
get_motif_probs() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
get_name() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
get_newick() (cogent3.core.tree.PhyloNode method)
get_newick_recursive() (cogent3.core.tree.PhyloNode method)
get_node_matching_name() (cogent3.core.tree.PhyloNode method)
get_node_names() (cogent3.core.tree.PhyloNode method)
get_nodes_dict() (cogent3.core.tree.PhyloNode method)
get_orf_positions() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
get_param_value() (cogent3.core.tree.PhyloNode method)
get_position_indices() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
get_projected_annotations() (cogent3.core.alignment.Alignment method)
get_region_covering_all() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
get_row_indices() (cogent3.util.table.Table method)
get_seq() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
get_seq_indices() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
get_similar() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
get_sub_alignment() (cogent3.core.alignment.ArrayAlignment method)
get_sub_tree() (cogent3.core.tree.PhyloNode method)
get_tip_names() (cogent3.core.tree.PhyloNode method)
get_translation() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
get_xml() (cogent3.core.tree.PhyloNode method)
gettype() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
H
has_terminal_stop() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
has_terminal_stops() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
head() (cogent3.util.table.Table method)
header() (cogent3.util.table.Table property)
I
index_in_parent() (cogent3.core.tree.PhyloNode method)
index_name() (cogent3.util.table.Table property)
information_plot() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
inner_join() (cogent3.util.table.Table method)
insert() (cogent3.core.tree.PhyloNode method)
is_annotated() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
is_array (cogent3.core.alignment.Alignment attribute)
(cogent3.core.alignment.ArrayAlignment attribute)
(cogent3.core.alignment.SequenceCollection attribute)
is_degenerate() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
is_gap() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
is_gapped() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
is_ragged() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
is_root() (cogent3.core.tree.PhyloNode method)
is_strict() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
is_tip() (cogent3.core.tree.PhyloNode method)
is_valid() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
isroot() (cogent3.core.tree.PhyloNode method)
istip() (cogent3.core.tree.PhyloNode method)
iter_nontips() (cogent3.core.tree.PhyloNode method)
iter_positions() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
iter_selected() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
iter_seqs() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
iter_tips() (cogent3.core.tree.PhyloNode method)
iupac_consensus() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
J
joined() (cogent3.util.table.Table method)
L
last_common_ancestor() (cogent3.core.tree.PhyloNode method)
lca() (cogent3.core.tree.PhyloNode method)
legend() (cogent3.util.table.Table property)
length() (cogent3.core.tree.PhyloNode property)
levelorder() (cogent3.core.tree.PhyloNode method)
line_wrap (cogent3.core.sequence.DnaSequence attribute)
(cogent3.core.sequence.ProteinSequence attribute)
(cogent3.core.sequence.RnaSequence attribute)
lowest_common_ancestor() (cogent3.core.tree.PhyloNode method)
M
majority_consensus() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
make_tree_array() (cogent3.core.tree.PhyloNode method)
matching_ref() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
matrix_distance() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
max_tip_tip_distance() (cogent3.core.tree.PhyloNode method)
moltype (cogent3.core.alignment.Alignment attribute)
(cogent3.core.alignment.ArrayAlignment attribute)
(cogent3.core.alignment.SequenceCollection attribute)
(cogent3.core.sequence.DnaSequence attribute)
(cogent3.core.sequence.ProteinSequence attribute)
(cogent3.core.sequence.RnaSequence attribute)
multifurcating() (cogent3.core.tree.PhyloNode method)
must_match() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
must_pair() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
mw() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
N
name_unnamed_nodes() (cogent3.core.tree.PhyloNode method)
named_seqs() (cogent3.core.alignment.ArrayAlignment property)
no_degenerates() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
non_tip_children() (cogent3.core.tree.PhyloNode method)
nontips() (cogent3.core.tree.PhyloNode method)
normalized() (cogent3.util.table.Table method)
num_seqs() (cogent3.core.alignment.Alignment property)
(cogent3.core.alignment.ArrayAlignment property)
(cogent3.core.alignment.SequenceCollection property)
O
omit_bad_seqs() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
omit_gap_pos() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
omit_gap_runs() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
omit_gap_seqs() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
P
pad_seqs() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
parent() (cogent3.core.tree.PhyloNode property)
parse_out_gaps() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
PhyloNode (class in cogent3.core.tree)
pop() (cogent3.core.tree.PhyloNode method)
positions() (cogent3.core.alignment.Alignment property)
(cogent3.core.alignment.ArrayAlignment property)
possibilities() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
postorder() (cogent3.core.tree.PhyloNode method)
pre_and_postorder() (cogent3.core.tree.PhyloNode method)
preorder() (cogent3.core.tree.PhyloNode method)
probs_per_pos() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
probs_per_seq() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
project_annotation() (cogent3.core.alignment.Alignment method)
PROTEIN (cogent3.core.sequence.DnaSequence attribute)
protein (cogent3.core.sequence.DnaSequence attribute)
PROTEIN (cogent3.core.sequence.RnaSequence attribute)
protein (cogent3.core.sequence.RnaSequence attribute)
ProteinSequence (class in cogent3.core.sequence)
prune() (cogent3.core.tree.PhyloNode method)
Q
quick_tree() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
R
rc() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
reassign_names() (cogent3.core.tree.PhyloNode method)
remove() (cogent3.core.tree.PhyloNode method)
remove_deleted() (cogent3.core.tree.PhyloNode method)
remove_node() (cogent3.core.tree.PhyloNode method)
rename_seqs() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
replace() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
replace_seqs() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
resolveambiguities() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
reverse_complement() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
RnaSequence (class in cogent3.core.sequence)
root() (cogent3.core.tree.PhyloNode method)
root_at_midpoint() (cogent3.core.tree.PhyloNode method)
rooted_at() (cogent3.core.tree.PhyloNode method)
rooted_with_tip() (cogent3.core.tree.PhyloNode method)
S
same_shape() (cogent3.core.tree.PhyloNode method)
same_topology() (cogent3.core.tree.PhyloNode method)
sample() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
scale_branch_lengths() (cogent3.core.tree.PhyloNode method)
separation() (cogent3.core.tree.PhyloNode method)
seqlogo() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
seqs() (cogent3.core.alignment.Alignment property)
(cogent3.core.alignment.ArrayAlignment property)
(cogent3.core.alignment.SequenceCollection property)
SequenceCollection (class in cogent3.core.alignment)
set_max_tip_tip_distance() (cogent3.core.tree.PhyloNode method)
set_param_value() (cogent3.core.tree.PhyloNode method)
set_repr_policy() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.util.table.Table method)
set_tip_distances() (cogent3.core.tree.PhyloNode method)
shape() (cogent3.util.table.Table property)
shuffle() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
siblings() (cogent3.core.tree.PhyloNode method)
sliding_windows() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
sorted() (cogent3.core.tree.PhyloNode method)
(cogent3.util.table.Table method)
space() (cogent3.util.table.Table property)
strand_symmetry() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
strip_bad() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
strip_bad_and_gaps() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
strip_degenerate() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
subset() (cogent3.core.tree.PhyloNode method)
subsets() (cogent3.core.tree.PhyloNode method)
sum_columns() (cogent3.util.table.Table method)
sum_rows() (cogent3.util.table.Table method)
summed() (cogent3.util.table.Table method)
T
Table (class in cogent3.util.table)
tail() (cogent3.util.table.Table method)
take_positions() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
take_positions_if() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
take_seqs() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
take_seqs_if() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
tip_children() (cogent3.core.tree.PhyloNode method)
tip_to_tip_distances() (cogent3.core.tree.PhyloNode method)
tips() (cogent3.core.tree.PhyloNode method)
tips_within_distance() (cogent3.core.tree.PhyloNode method)
title() (cogent3.util.table.Table property)
to_csv() (cogent3.util.table.Table method)
to_dataframe() (cogent3.util.table.Table method)
to_dict() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.util.table.Table method)
to_dna() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
to_fasta() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
to_html() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
to_json() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
(cogent3.core.tree.PhyloNode method)
(cogent3.util.table.Table method)
to_latex() (cogent3.util.table.Table method)
to_markdown() (cogent3.util.table.Table method)
to_moltype() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
to_nexus() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
to_phylip() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
to_plotly() (cogent3.util.table.Table method)
to_pretty() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
to_protein() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
to_rich_dict() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
(cogent3.core.tree.PhyloNode method)
(cogent3.util.table.Table method)
to_rich_html() (cogent3.util.table.Table method)
to_rna() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
to_rst() (cogent3.util.table.Table method)
to_string() (cogent3.util.table.Table method)
to_tsv() (cogent3.util.table.Table method)
to_type() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
tolist() (cogent3.util.table.Table method)
total_descending_branch_length() (cogent3.core.tree.PhyloNode method)
total_length() (cogent3.core.tree.PhyloNode method)
translate() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
transposed() (cogent3.util.table.Table method)
traverse() (cogent3.core.tree.PhyloNode method)
traverse_recursive() (cogent3.core.tree.PhyloNode method)
trim_stop_codon() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
trim_stop_codons() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
U
unrooted() (cogent3.core.tree.PhyloNode method)
unrooted_deepcopy() (cogent3.core.tree.PhyloNode method)
V
variable_positions() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
W
with_gaps_from() (cogent3.core.alignment.Alignment method)
with_masked_annotations() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
with_modified_termini() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
with_new_column() (cogent3.util.table.Table method)
with_new_header() (cogent3.util.table.Table method)
with_termini_unknown() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.ProteinSequence method)
(cogent3.core.sequence.RnaSequence method)
write() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
(cogent3.core.tree.PhyloNode method)
(cogent3.util.table.Table method)