cogent3
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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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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
A
add_annotation() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
add_feature() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence 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.RnaSequence method)
annotate_matches_to() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
annotations (cogent3.core.alignment.Alignment attribute)
(cogent3.core.sequence.DnaSequence 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)
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.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.RnaSequence method)
can_mismatch() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
can_mispair() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
can_pair() (cogent3.core.sequence.DnaSequence 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.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)
cogent3.util.misc
col_sum() (cogent3.util.table.Table method)
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.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.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.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.RnaSequence method)
(cogent3.util.table.Table method)
count_degenerate() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
count_gaps() (cogent3.core.sequence.DnaSequence 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)
counts() (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)
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)
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.RnaSequence method)
descendant_array() (cogent3.core.tree.PhyloNode method)
detach_annotations() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
diff() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
disambiguate() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
distance() (cogent3.core.sequence.DnaSequence 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.RnaSequence method)
first_gap() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
first_invalid() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
first_non_strict() (cogent3.core.sequence.DnaSequence 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.RnaSequence method)
frac_diff_gaps() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
frac_diff_non_gaps() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
frac_same() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
frac_same_gaps() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
frac_same_non_gaps() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
frac_similar() (cogent3.core.sequence.DnaSequence 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.RnaSequence method)
gap_maps() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
gap_vector() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
gapped_by_map() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
gapped_by_map_motif_iter() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
gapped_by_map_segment_iter() (cogent3.core.sequence.DnaSequence 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.RnaSequence method)
get_by_annotation() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence 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.RnaSequence method)
get_colour_scheme() (cogent3.core.sequence.DnaSequence 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.RnaSequence method)
get_drawables() (cogent3.core.alignment.Alignment method)
(cogent3.core.sequence.DnaSequence 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.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.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.RnaSequence 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.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)
information_plot() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
insert() (cogent3.core.tree.PhyloNode method)
is_annotated() (cogent3.core.sequence.DnaSequence 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.RnaSequence method)
is_gap() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
is_gapped() (cogent3.core.sequence.DnaSequence 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.RnaSequence method)
is_tip() (cogent3.core.tree.PhyloNode method)
is_valid() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
isroot() (cogent3.core.tree.PhyloNode method)
istip() (cogent3.core.tree.PhyloNode method)
items() (cogent3.util.table.Table 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)
K
keys() (cogent3.util.table.Table method)
L
last_common_ancestor() (cogent3.core.tree.PhyloNode method)
lca() (cogent3.core.tree.PhyloNode method)
length() (cogent3.core.tree.PhyloNode property)
levelorder() (cogent3.core.tree.PhyloNode method)
line_wrap (cogent3.core.sequence.DnaSequence 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.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.RnaSequence attribute)
multifurcating() (cogent3.core.tree.PhyloNode method)
must_match() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
must_pair() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
mw() (cogent3.core.sequence.DnaSequence 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.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.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)
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.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.RnaSequence method)
replace_seqs() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
resolveambiguities() (cogent3.core.sequence.DnaSequence 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)
row_sum() (cogent3.util.table.Table 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)
shuffle() (cogent3.core.sequence.DnaSequence 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.RnaSequence method)
sorted() (cogent3.core.tree.PhyloNode method)
(cogent3.util.table.Table method)
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.RnaSequence method)
strip_bad() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
strip_bad_and_gaps() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
strip_degenerate() (cogent3.core.sequence.DnaSequence method)
(cogent3.core.sequence.RnaSequence method)
subset() (cogent3.core.tree.PhyloNode method)
subsets() (cogent3.core.tree.PhyloNode 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)
to_array() (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.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.RnaSequence method)
(cogent3.core.tree.PhyloNode method)
(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.RnaSequence method)
to_nexus() (cogent3.core.alignment.Alignment method)
(cogent3.core.alignment.ArrayAlignment method)
(cogent3.core.alignment.SequenceCollection method)
to_normalized() (cogent3.util.table.Table 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.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_string() (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.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.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.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.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)