Index

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

_

__bool__() (skbio.alignment.TabularMSA method)
(skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
__call__() (skbio.workflow.method method)
(skbio.workflow.Workflow method)
(skbio.workflow.requires method)
__contains__() (skbio.alignment.TabularMSA method)
(skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
(skbio.stats.distance.DissimilarityMatrix method)
(skbio.stats.distance.DistanceMatrix method)
__copy__() (skbio.alignment.TabularMSA method)
(skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
(skbio.tree.TreeNode method)
__deepcopy__() (skbio.alignment.TabularMSA method)
(skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
(skbio.tree.TreeNode method)
__eq__() (skbio.alignment.TabularMSA method)
(skbio.sequence.DNA method)
(skbio.sequence.GeneticCode method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
(skbio.stats.distance.DissimilarityMatrix method)
(skbio.stats.distance.DistanceMatrix method)
__format__() (skbio.alignment.AlignmentStructure method)
(skbio.alignment.TabularMSA method)
(skbio.io.registry.Format method)
(skbio.io.registry.IORegistry method)
(skbio.sequence.DNA method)
(skbio.sequence.GeneticCode method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
(skbio.stats.distance.DissimilarityMatrix method)
(skbio.stats.distance.DistanceMatrix method)
(skbio.stats.gradient.AverageGradientANOVA method)
(skbio.stats.gradient.CategoryResults method)
(skbio.stats.gradient.FirstDifferenceGradientANOVA method)
(skbio.stats.gradient.GradientANOVA method)
(skbio.stats.gradient.GradientANOVAResults method)
(skbio.stats.gradient.GroupResults method)
(skbio.stats.gradient.TrajectoryGradientANOVA method)
(skbio.stats.gradient.WindowDifferenceGradientANOVA method)
(skbio.tree.TreeNode method)
(skbio.util.TestRunner method)
(skbio.workflow.Workflow method)
(skbio.workflow.method method)
(skbio.workflow.requires method)
__getitem__() (skbio.alignment.TabularMSA method)
(skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
(skbio.stats.distance.DissimilarityMatrix method)
(skbio.stats.distance.DistanceMatrix method)
(skbio.tree.TreeNode method)
__iter__() (skbio.alignment.TabularMSA method)
(skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
(skbio.tree.TreeNode method)
__len__() (skbio.alignment.TabularMSA method)
(skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
(skbio.tree.TreeNode method)
__ne__() (skbio.alignment.TabularMSA method)
(skbio.sequence.DNA method)
(skbio.sequence.GeneticCode method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
(skbio.stats.distance.DissimilarityMatrix method)
(skbio.stats.distance.DistanceMatrix method)
__nonzero__() (skbio.alignment.TabularMSA method)
(skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
__reversed__() (skbio.alignment.TabularMSA method)
(skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
__str__() (skbio.alignment.TabularMSA method)
(skbio.sequence.DNA method)
(skbio.sequence.GeneticCode method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
(skbio.stats.distance.DissimilarityMatrix method)
(skbio.stats.distance.DistanceMatrix method)
(skbio.tree.TreeNode method)

A

accumulate_to_ancestor() (skbio.tree.TreeNode method)
ace() (in module skbio.diversity.alpha)
add_format() (skbio.io.registry.IORegistry method)
aligned_query_sequence (skbio.alignment.AlignmentStructure attribute)
aligned_target_sequence (skbio.alignment.AlignmentStructure attribute)
AlignmentStructure (class in skbio.alignment)
alpha_diversity() (in module skbio.diversity)
alphabet (skbio.sequence.DNA attribute)
(skbio.sequence.Protein attribute)
(skbio.sequence.RNA attribute)
ancestors() (skbio.tree.TreeNode method)
ancom() (in module skbio.stats.composition)
anosim() (in module skbio.stats.distance)
append() (skbio.alignment.TabularMSA method)
(skbio.tree.TreeNode method)
ArgumentOverrideWarning
ascii_art() (skbio.tree.TreeNode method)
assert_data_frame_almost_equal() (in module skbio.util)
assert_ordination_results_equal() (in module skbio.util)
assign_ids() (skbio.tree.TreeNode method)
AverageGradientANOVA (class in skbio.stats.gradient)

B

berger_parker_d() (in module skbio.diversity.alpha)
beta_diversity() (in module skbio.diversity)
bioenv() (in module skbio.stats.distance)
BLAST7FormatError
brillouin_d() (in module skbio.diversity.alpha)

C

ca() (in module skbio.stats.ordination)
cache_attr() (skbio.tree.TreeNode method)
cardinal_to_ordinal() (in module skbio.util)
CategoryResults (class in skbio.stats.gradient)
cca() (in module skbio.stats.ordination)
centralize() (in module skbio.stats.composition)
chao1() (in module skbio.diversity.alpha)
chao1_ci() (in module skbio.diversity.alpha)
cigar (skbio.alignment.AlignmentStructure attribute)
closure() (in module skbio.stats.composition)
clr() (in module skbio.stats.composition)
clr_inv() (in module skbio.stats.composition)
ClustalFormatError
compare_rfd() (skbio.tree.TreeNode method)
compare_subsets() (skbio.tree.TreeNode method)
compare_tip_distances() (skbio.tree.TreeNode method)
complement() (skbio.sequence.DNA method)
(skbio.sequence.RNA method)
complement_map (skbio.sequence.DNA attribute)
(skbio.sequence.RNA attribute)
concat() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence class method)
condensed_form() (skbio.stats.distance.DistanceMatrix method)
confidence_bound() (in module skbio.stats.power)
consensus() (skbio.alignment.TabularMSA method)
conservation() (skbio.alignment.TabularMSA method)
copy() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
(skbio.stats.distance.DissimilarityMatrix method)
(skbio.stats.distance.DistanceMatrix method)
(skbio.tree.TreeNode method)
corr() (in module skbio.stats.ordination)
count() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
(skbio.tree.TreeNode method)
create_caches() (skbio.tree.TreeNode method)
create_dir() (in module skbio.util)
create_format() (in module skbio.io.registry)
(skbio.io.registry.IORegistry method)

D

data (skbio.stats.distance.DissimilarityMatrix attribute)
(skbio.stats.distance.DistanceMatrix attribute)
deepcopy() (skbio.tree.TreeNode method)
default_gap_char (skbio.sequence.DNA attribute)
(skbio.sequence.Protein attribute)
(skbio.sequence.RNA attribute)
default_write_format (skbio.alignment.TabularMSA attribute)
(skbio.sequence.DNA attribute)
(skbio.sequence.Protein attribute)
(skbio.sequence.RNA attribute)
(skbio.sequence.Sequence attribute)
(skbio.stats.distance.DissimilarityMatrix attribute)
(skbio.stats.distance.DistanceMatrix attribute)
(skbio.tree.TreeNode attribute)
degap() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
degenerate_chars (skbio.sequence.DNA attribute)
(skbio.sequence.Protein attribute)
(skbio.sequence.RNA attribute)
degenerate_map (skbio.sequence.DNA attribute)
(skbio.sequence.Protein attribute)
(skbio.sequence.RNA attribute)
degenerates() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
descending_branch_length() (skbio.tree.TreeNode method)
DissimilarityMatrix (class in skbio.stats.distance)
DissimilarityMatrixError
distance() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
(skbio.tree.TreeNode method)
DistanceMatrix (class in skbio.stats.distance)
DistanceMatrixError
DNA (class in skbio.sequence)
dominance() (in module skbio.diversity.alpha)
doubles() (in module skbio.diversity.alpha)
dtype (skbio.alignment.TabularMSA attribute)
(skbio.stats.distance.DissimilarityMatrix attribute)
(skbio.stats.distance.DistanceMatrix attribute)
DuplicateNodeError
DuplicateRegistrationError

E

EfficiencyWarning
enspie() (in module skbio.diversity.alpha)
esty_ci() (in module skbio.diversity.alpha)
expand_degenerates() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
extend() (skbio.alignment.TabularMSA method)
(skbio.tree.TreeNode method)

F

faith_pd() (in module skbio.diversity.alpha)
FASTAFormatError
FASTQFormatError
FileFormatError
filter() (skbio.stats.distance.DissimilarityMatrix method)
(skbio.stats.distance.DistanceMatrix method)
find() (skbio.tree.TreeNode method)
find_all() (skbio.tree.TreeNode method)
find_by_func() (skbio.tree.TreeNode method)
find_by_id() (skbio.tree.TreeNode method)
find_duplicates() (in module skbio.util)
find_motifs() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
find_with_regex() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
FirstDifferenceGradientANOVA (class in skbio.stats.gradient)
fisher_alpha() (in module skbio.diversity.alpha)
Format (class in skbio.io.registry)
FormatIdentificationWarning
frequencies() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
from_dict() (skbio.alignment.TabularMSA class method)
from_iterable() (skbio.stats.distance.DistanceMatrix class method)
from_linkage_matrix() (skbio.tree.TreeNode class method)
from_ncbi() (skbio.sequence.GeneticCode class method)
from_taxonomy() (skbio.tree.TreeNode class method)

G

gap_chars (skbio.sequence.DNA attribute)
(skbio.sequence.Protein attribute)
(skbio.sequence.RNA attribute)
gap_frequencies() (skbio.alignment.TabularMSA method)
gaps() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
gc_content() (skbio.sequence.DNA method)
(skbio.sequence.RNA method)
gc_frequency() (skbio.sequence.DNA method)
(skbio.sequence.RNA method)
GeneticCode (class in skbio.sequence)
get_alpha_diversity_metrics() (in module skbio.diversity)
get_beta_diversity_metrics() (in module skbio.diversity)
get_data_path() (in module skbio.util)
get_max_distance() (skbio.tree.TreeNode method)
get_reader() (skbio.io.registry.IORegistry method)
get_sniffer() (skbio.io.registry.IORegistry method)
get_trajectories() (skbio.stats.gradient.AverageGradientANOVA method)
(skbio.stats.gradient.FirstDifferenceGradientANOVA method)
(skbio.stats.gradient.GradientANOVA method)
(skbio.stats.gradient.TrajectoryGradientANOVA method)
(skbio.stats.gradient.WindowDifferenceGradientANOVA method)
get_writer() (skbio.io.registry.IORegistry method)
gini_index() (in module skbio.diversity.alpha)
global_pairwise_align() (in module skbio.alignment)
global_pairwise_align_nucleotide() (in module skbio.alignment)
global_pairwise_align_protein() (in module skbio.alignment)
goods_coverage() (in module skbio.diversity.alpha)
GradientANOVA (class in skbio.stats.gradient)
GradientANOVAResults (class in skbio.stats.gradient)
GroupResults (class in skbio.stats.gradient)

H

has_children() (skbio.tree.TreeNode method)
has_degenerates() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
has_gaps() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
has_metadata() (skbio.alignment.TabularMSA method)
(skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
has_nondegenerates() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
has_positional_metadata() (skbio.alignment.TabularMSA method)
(skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
has_stops() (skbio.sequence.Protein method)
heip_e() (in module skbio.diversity.alpha)
highest_priority (skbio.workflow.method attribute)
hommola_cospeciation() (in module skbio.stats.evolve)

I

ids (skbio.stats.distance.DissimilarityMatrix attribute)
(skbio.stats.distance.DistanceMatrix attribute)
iloc (skbio.alignment.TabularMSA attribute)
ilr() (in module skbio.stats.composition)
ilr_inv() (in module skbio.stats.composition)
index (skbio.alignment.TabularMSA attribute)
index() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
(skbio.stats.distance.DissimilarityMatrix method)
(skbio.stats.distance.DistanceMatrix method)
index_tree() (skbio.tree.TreeNode method)
initialize_state() (skbio.workflow.Workflow method)
inner() (in module skbio.stats.composition)
invalidate_caches() (skbio.tree.TreeNode method)
InvalidRegistrationError
IORegistry (class in skbio.io.registry)
IOSourceError
is_binary_format (skbio.io.registry.Format attribute)
is_casava_v180_or_later() (in module skbio.util)
is_reverse_complement() (skbio.sequence.DNA method)
(skbio.sequence.RNA method)
is_root() (skbio.tree.TreeNode method)
is_tip() (skbio.tree.TreeNode method)
is_zero_based() (skbio.alignment.AlignmentStructure method)
isubsample() (in module skbio.stats)
iter_contiguous() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
iter_kmers() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
iter_positions() (skbio.alignment.TabularMSA method)

J

join() (skbio.alignment.TabularMSA method)

K

kempton_taylor_q() (in module skbio.diversity.alpha)
kmer_frequencies() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)

L

lca() (skbio.tree.TreeNode method)
levelorder() (skbio.tree.TreeNode method)
list_read_formats() (skbio.io.registry.IORegistry method)
list_write_formats() (skbio.io.registry.IORegistry method)
lladser_ci() (in module skbio.diversity.alpha)
lladser_pe() (in module skbio.diversity.alpha)
loc (skbio.alignment.TabularMSA attribute)
local_pairwise_align() (in module skbio.alignment)
local_pairwise_align_nucleotide() (in module skbio.alignment)
local_pairwise_align_protein() (in module skbio.alignment)
local_pairwise_align_ssw() (in module skbio.alignment)
lowercase() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
lowest_common_ancestor() (skbio.tree.TreeNode method)
LSMatFormatError

M

majority_rule() (in module skbio.tree)
make_identity_substitution_matrix() (in module skbio.alignment)
mantel() (in module skbio.stats.distance)
margalef() (in module skbio.diversity.alpha)
match_frequency() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
matches() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
mcintosh_d() (in module skbio.diversity.alpha)
mcintosh_e() (in module skbio.diversity.alpha)
mean_and_std() (in module skbio.stats.ordination)
menhinick() (in module skbio.diversity.alpha)
metadata (skbio.alignment.TabularMSA attribute)
(skbio.sequence.DNA attribute)
(skbio.sequence.Protein attribute)
(skbio.sequence.RNA attribute)
(skbio.sequence.Sequence attribute)
method (class in skbio.workflow)
michaelis_menten_fit() (in module skbio.diversity.alpha)
mismatch_frequency() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
mismatches() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
MissingIDError
MissingNodeError
monkey_patch() (skbio.io.registry.IORegistry method)
monkey_patched_readers (skbio.io.registry.Format attribute)
monkey_patched_writers (skbio.io.registry.Format attribute)
multiplicative_replacement() (in module skbio.stats.composition)

N

name (skbio.io.registry.Format attribute)
(skbio.sequence.GeneticCode attribute)
neighbors() (skbio.tree.TreeNode method)
NewickFormatError
nj() (in module skbio.tree)
NoLengthError
non_tips() (skbio.tree.TreeNode method)
nondegenerate_chars (skbio.sequence.DNA attribute)
(skbio.sequence.Protein attribute)
(skbio.sequence.RNA attribute)
nondegenerates() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
NoParentError

O

observed_chars (skbio.sequence.DNA attribute)
(skbio.sequence.Protein attribute)
(skbio.sequence.RNA attribute)
(skbio.sequence.Sequence attribute)
observed_node_counts() (skbio.tree.TreeNode method)
observed_otus() (in module skbio.diversity.alpha)
open() (in module skbio.io.util)
open_file() (in module skbio.io.util)
open_files() (in module skbio.io.util)
optimal_alignment_score (skbio.alignment.AlignmentStructure attribute)
OrdinationFormatError
osd() (in module skbio.diversity.alpha)

P

paired_subsamples() (in module skbio.stats.power)
pcoa() (in module skbio.stats.ordination)
permanova() (in module skbio.stats.distance)
permute() (skbio.stats.distance.DistanceMatrix method)
perturb() (in module skbio.stats.composition)
perturb_inv() (in module skbio.stats.composition)
PhylipFormatError
pielou_e() (in module skbio.diversity.alpha)
plot() (skbio.stats.distance.DissimilarityMatrix method)
(skbio.stats.distance.DistanceMatrix method)
png (skbio.stats.distance.DissimilarityMatrix attribute)
(skbio.stats.distance.DistanceMatrix attribute)
pop() (skbio.tree.TreeNode method)
positional_metadata (skbio.alignment.TabularMSA attribute)
(skbio.sequence.DNA attribute)
(skbio.sequence.Protein attribute)
(skbio.sequence.RNA attribute)
(skbio.sequence.Sequence attribute)
postorder() (skbio.tree.TreeNode method)
power() (in module skbio.stats.composition)
pre_and_postorder() (skbio.tree.TreeNode method)
preorder() (skbio.tree.TreeNode method)
Protein (class in skbio.sequence)
prune() (skbio.tree.TreeNode method)
pwmantel() (in module skbio.stats.distance)

Q

QSeqFormatError
QUALFormatError
query_begin (skbio.alignment.AlignmentStructure attribute)
query_end (skbio.alignment.AlignmentStructure attribute)
query_sequence (skbio.alignment.AlignmentStructure attribute)

R

randdm() (in module skbio.stats.distance)
rda() (in module skbio.stats.ordination)
read() (in module skbio.io.registry)
(skbio.alignment.TabularMSA class method)
(skbio.io.registry.IORegistry method)
(skbio.sequence.DNA class method)
(skbio.sequence.Protein class method)
(skbio.sequence.RNA class method)
(skbio.sequence.Sequence class method)
(skbio.stats.distance.DissimilarityMatrix class method)
(skbio.stats.distance.DistanceMatrix class method)
(skbio.tree.TreeNode class method)
reader() (skbio.io.registry.Format method)
readers (skbio.io.registry.Format attribute)
reading_frames (skbio.sequence.GeneticCode attribute)
reassign_index() (skbio.alignment.TabularMSA method)
redundant_form() (skbio.stats.distance.DissimilarityMatrix method)
(skbio.stats.distance.DistanceMatrix method)
remove() (skbio.tree.TreeNode method)
remove_deleted() (skbio.tree.TreeNode method)
remove_files() (in module skbio.util)
RepresentationWarning
requires (class in skbio.workflow)
reverse_complement() (skbio.sequence.DNA method)
(skbio.sequence.RNA method)
reverse_transcribe() (skbio.sequence.RNA method)
RNA (class in skbio.sequence)
robbins() (in module skbio.diversity.alpha)
root() (skbio.tree.TreeNode method)
root_at() (skbio.tree.TreeNode method)
root_at_midpoint() (skbio.tree.TreeNode method)

S

safe_md5() (in module skbio.util)
scale() (in module skbio.stats.ordination)
Sequence (class in skbio.sequence)
set_zero_based() (skbio.alignment.AlignmentStructure method)
shannon() (in module skbio.diversity.alpha)
shape (skbio.alignment.TabularMSA attribute)
(skbio.stats.distance.DissimilarityMatrix attribute)
(skbio.stats.distance.DistanceMatrix attribute)
shear() (skbio.tree.TreeNode method)
shuffle() (skbio.tree.TreeNode method)
siblings() (skbio.tree.TreeNode method)
simpson() (in module skbio.diversity.alpha)
simpson_e() (in module skbio.diversity.alpha)
singles() (in module skbio.diversity.alpha)
size (skbio.stats.distance.DissimilarityMatrix attribute)
(skbio.stats.distance.DistanceMatrix attribute)
skbio.alignment (module)
skbio.diversity (module)
skbio.diversity.alpha (module)
skbio.diversity.beta (module)
skbio.io (module)
skbio.io.format.blast6 (module)
skbio.io.format.blast7 (module)
skbio.io.format.clustal (module)
skbio.io.format.fasta (module)
skbio.io.format.fastq (module)
skbio.io.format.lsmat (module)
skbio.io.format.newick (module)
skbio.io.format.ordination (module)
skbio.io.format.phylip (module)
skbio.io.format.qseq (module)
skbio.io.registry (module)
skbio.io.util (module)
skbio.sequence (module)
skbio.stats (module)
skbio.stats.composition (module)
skbio.stats.distance (module)
skbio.stats.evolve (module)
skbio.stats.gradient (module)
skbio.stats.ordination (module)
skbio.stats.power (module)
skbio.tree (module)
skbio.util (module)
skbio.workflow (module)
sniff() (in module skbio.io.registry)
(skbio.io.registry.IORegistry method)
sniffer() (skbio.io.registry.Format method)
sniffer_function (skbio.io.registry.Format attribute)
sort() (skbio.alignment.TabularMSA method)
stop_chars (skbio.sequence.Protein attribute)
stops() (skbio.sequence.Protein method)
StripedSmithWaterman (class in skbio.alignment)
strong() (in module skbio.diversity.alpha)
suboptimal_alignment_score (skbio.alignment.AlignmentStructure attribute)
subsample_counts() (in module skbio.stats)
subsample_paired_power() (in module skbio.stats.power)
subsample_power() (in module skbio.stats.power)
subset() (skbio.tree.TreeNode method)
subsets() (skbio.tree.TreeNode method)
subtree() (skbio.tree.TreeNode method)
svd_rank() (in module skbio.stats.ordination)
svg (skbio.stats.distance.DissimilarityMatrix attribute)
(skbio.stats.distance.DistanceMatrix attribute)

T

T (skbio.stats.distance.DissimilarityMatrix attribute)
(skbio.stats.distance.DistanceMatrix attribute)
TabularMSA (class in skbio.alignment)
target_begin (skbio.alignment.AlignmentStructure attribute)
target_end_optimal (skbio.alignment.AlignmentStructure attribute)
target_end_suboptimal (skbio.alignment.AlignmentStructure attribute)
target_sequence (skbio.alignment.AlignmentStructure attribute)
test() (skbio.util.TestRunner method)
TestRunner (class in skbio.util)
tip_tip_distances() (skbio.tree.TreeNode method)
tips() (skbio.tree.TreeNode method)
to_array() (skbio.tree.TreeNode method)
to_data_frame() (skbio.stats.distance.DissimilarityMatrix method)
(skbio.stats.distance.DistanceMatrix method)
to_dict() (skbio.alignment.TabularMSA method)
to_files() (skbio.stats.gradient.CategoryResults method)
(skbio.stats.gradient.GradientANOVAResults method)
(skbio.stats.gradient.GroupResults method)
to_regex() (skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
to_taxonomy() (skbio.tree.TreeNode method)
TrajectoryGradientANOVA (class in skbio.stats.gradient)
transcribe() (skbio.sequence.DNA method)
translate() (skbio.sequence.DNA method)
(skbio.sequence.GeneticCode method)
(skbio.sequence.RNA method)
translate_six_frames() (skbio.sequence.DNA method)
(skbio.sequence.GeneticCode method)
(skbio.sequence.RNA method)
transpose() (skbio.stats.distance.DissimilarityMatrix method)
(skbio.stats.distance.DistanceMatrix method)
traverse() (skbio.tree.TreeNode method)
TreeError
TreeNode (class in skbio.tree)

U

UnrecognizedFormatError
unrooted_copy() (skbio.tree.TreeNode method)
unrooted_deepcopy() (skbio.tree.TreeNode method)
unweighted_unifrac() (in module skbio.diversity.beta)

V

values (skbio.sequence.DNA attribute)
(skbio.sequence.Protein attribute)
(skbio.sequence.RNA attribute)
(skbio.sequence.Sequence attribute)

W

weighted_unifrac() (in module skbio.diversity.beta)
WindowDifferenceGradientANOVA (class in skbio.stats.gradient)
Workflow (class in skbio.workflow)
write() (in module skbio.io.registry)
(skbio.alignment.TabularMSA method)
(skbio.io.registry.IORegistry method)
(skbio.sequence.DNA method)
(skbio.sequence.Protein method)
(skbio.sequence.RNA method)
(skbio.sequence.Sequence method)
(skbio.stats.distance.DissimilarityMatrix method)
(skbio.stats.distance.DistanceMatrix method)
(skbio.tree.TreeNode method)
writer() (skbio.io.registry.Format method)
writers (skbio.io.registry.Format attribute)