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	licenses
cogent3	align_to_ref	True	Aligns sequences to a nominated reference in the unaligned collection.	SequenceCollection	Alignment, ByteSequence, DictArray, DistanceMatrix, DnaSequence, PhyloNode, ProteinSequence, ProteinWithStopSequence, RnaSequence, Sequence, SequenceCollection, SerialisableType, Table, bootstrap_result, generic_result, hypothesis_result, model_result, tabular_result	BSD
cogent3	ancestral_states	True	Computes ancestral state probabilities from a model result.	model_result	Alignment, ByteSequence, DictArray, DistanceMatrix, DnaSequence, PhyloNode, ProteinSequence, ProteinWithStopSequence, RnaSequence, Sequence, SequenceCollection, SerialisableType, Table, bootstrap_result, generic_result, hypothesis_result, model_result, tabular_result	BSD
cogent3	approx_jc69	True	Converts p-distances and returns pairwise JC69 distances	DistanceMatrix	DistanceMatrix	BSD
cogent3	approx_pdist	True	Calculates an approximation of the p-distance between sequences based on Jaccard distances (see Notes for details).	DistanceMatrix	DistanceMatrix	BSD
cogent3	bootstrap	True	Parametric bootstrap for a provided hypothesis.	Alignment	Alignment, ByteSequence, DictArray, DistanceMatrix, DnaSequence, PhyloNode, ProteinSequence, ProteinWithStopSequence, RnaSequence, Sequence, SequenceCollection, SerialisableType, Table, bootstrap_result, generic_result, hypothesis_result, model_result, tabular_result	BSD
...	...	...	...	...	...	...
piqtree	piq_jc_distances	True		Alignment	DistanceMatrix	GPL-2.0-only
piqtree	piq_model_finder	True	Find the models of best fit for an alignment using ModelFinder.	Alignment	ModelFinderResult	GPL-2.0-only
piqtree	piq_nj_tree	True	Construct a neighbour joining tree from a pairwise distance matrix.	DistanceMatrix	PhyloNode	GPL-2.0-only
piqtree	piq_random_tree	True	Generate a random phylogenetic tree.	int	PhyloNode	GPL-2.0-only
piqtree	piq_simulate_alignment	True	Uses AliSim to simulate an Alignment through IQ-TREE.	PhyloNode	Alignment	GPL-2.0-only

Top 5 and bottom 5 rows from 54 rows x 7 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	licenses
cogent3	load_aligned	True	Loads aligned sequences. Returns an Alignment object.	IdentifierType	Alignment, ByteSequence, DictArray, DistanceMatrix, DnaSequence, PhyloNode, ProteinSequence, ProteinWithStopSequence, RnaSequence, Sequence, SequenceCollection, SerialisableType, Table, bootstrap_result, generic_result, hypothesis_result, model_result, tabular_result	BSD
cogent3	load_db	True	Loads serialised cogent3 objects from a db. Returns whatever object type was stored.	IdentifierType	Alignment, ByteSequence, DictArray, DistanceMatrix, DnaSequence, PhyloNode, ProteinSequence, ProteinWithStopSequence, RnaSequence, Sequence, SequenceCollection, SerialisableType, Table, bootstrap_result, generic_result, hypothesis_result, model_result, tabular_result	BSD
cogent3	load_json	True	Loads json serialised cogent3 objects from a json file. Returns whatever object type was stored.	IdentifierType	Alignment, ByteSequence, DictArray, DistanceMatrix, DnaSequence, PhyloNode, ProteinSequence, ProteinWithStopSequence, RnaSequence, Sequence, SequenceCollection, SerialisableType, Table, bootstrap_result, generic_result, hypothesis_result, model_result, tabular_result	BSD
cogent3	load_tabular	True	Loads delimited data. Returns a Table.	IdentifierType	DictArray, DistanceMatrix, Table	BSD
cogent3	load_unaligned	True	Loads unaligned sequences. Returns a SequenceCollection.	IdentifierType	Alignment, ByteSequence, DictArray, DistanceMatrix, DnaSequence, PhyloNode, ProteinSequence, ProteinWithStopSequence, RnaSequence, Sequence, SequenceCollection, SerialisableType, Table, bootstrap_result, generic_result, hypothesis_result, model_result, tabular_result	BSD

5 rows x 7 columns

Note

The first column lists the package providing the app.