conda
apps
NotCompleted
progressive_align
info
model
model_result
tabulate_stats
ancestral_states
hypothesis
hypothesis_result
natsel
natsel_neutral
natsel_timehet
natsel_sitehet
natsel_zhang
user_function
Alignment
ArrayAlignment
Sequence
as_one_span
MolType
Alphabet
get_code()
CodonAlphabet
DnaSequence
ascii_art()
load_delimited()
FilteringParser
dict
pandas.DataFrame
head()
tail()
repr()
str()
to_string()
cogent3
alignment.quick_tree()
DistanceMatrix
cogent3.phylo.nj.nj()`
get_model()
UnionDict
list
tuple
kappa
app.apply_to()
cogent3.util.parallel.map()
alignment
sequence
genetic_code
moltype
alphabet
table
tree
x
We use Plotly as our backend for visualisation. It provides excellent graph interactivity in Jupyter notebooks.
Evaluating coevolution¶
Dotplot¶
Dotplot with annotated sequences¶
Counting gaps per sequence¶
Information analysis of an alignment¶
Draw sequence logos¶
Display a Phylogenetic Tree with a Angular Dendrogram Style¶
Display a Phylogenetic Tree with a Circular Dendrogram Style¶
Display a Phylogenetic Tree with a Radial Dendrogram Style¶
Display a Phylogenetic Tree with a Square Dendrogram Style¶
Display a Phylogenetic Tree Showing Bootstrap Support¶
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