Displaying installed apps

Apps perform functions ranging from multiple sequence alignment (e.g. progressive_align), to excluding alignment columns containing non-nucleotide characters (e.g. omit_degenerates) to performing maximum-likelihood evolutionary analyses (e.g. model).

from cogent3 import available_apps

available_apps()

package	name	composable	doc	input type	output type
cogent3	align_to_ref	True	Aligns sequences to a nominated reference in the unaligned collection.	SequenceCollection	Alignment, ArrayAlignment, SerialisableType
cogent3	ancestral_states	True	Computes ancestral state probabilities from a model result.	model_result	SerialisableType, tabular_result
cogent3	approx_jc69	True	Converts p-distances and returns pairwise JC69 distances	DistanceMatrix	DistanceMatrix
cogent3	approx_pdist	True	Calculates an approximation of the p-distance between sequences based on Jaccard distances (see Notes for details).	DistanceMatrix	DistanceMatrix
cogent3	bootstrap	True	Parametric bootstrap for a provided hypothesis.	Alignment, ArrayAlignment	SerialisableType, bootstrap_result
...	...	...	...	...	...
piqtree	piqtree_jc_dists	True		Alignment, ArrayAlignment	PhyloNode, SerialisableType
piqtree	piqtree_mfinder	True	Find the models of best fit for an alignment using ModelFinder.	Alignment, ArrayAlignment	ModelFinderResult, SerialisableType
piqtree	piqtree_nj	True	Construct a neighbour joining tree from a pairwise distance matrix.	DistanceMatrix	PhyloNode
piqtree	piqtree_phylo	True		Alignment, ArrayAlignment	PhyloNode, SerialisableType
piqtree	piqtree_random_trees	True	Generate a collection of random trees.	int	PhyloNode

Top 5 and bottom 5 rows from 52 rows x 6 columns

The name_filter argument can be used to display only the apps that match a string. For example, to display all the loader apps

available_apps(name_filter="load")

package	name	composable	doc	input type	output type
cogent3	load_aligned	True	Loads aligned sequences. Returns an Alignment object.	IdentifierType	Alignment, ArrayAlignment, SerialisableType
cogent3	load_db	True	Loads serialised cogent3 objects from a db. Returns whatever object type was stored.	IdentifierType	SerialisableType
cogent3	load_json	True	Loads json serialised cogent3 objects from a json file. Returns whatever object type was stored.	IdentifierType	SerialisableType
cogent3	load_tabular	True	Loads delimited data. Returns a Table.	IdentifierType	DictArray, DistanceMatrix, Table
cogent3	load_unaligned	True	Loads unaligned sequences. Returns a SequenceCollection.	IdentifierType	SequenceCollection, SerialisableType

5 rows x 6 columns

Note

The first column lists the package providing the app.