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
cogent3	cogent3_score	True	returns the cogent3 log-likelihood as an alignment quality score	Alignment, ArrayAlignment	float
cogent3	concat	False	Creates a concatenated alignment from a series.	Alignment, ArrayAlignment	Alignment, ArrayAlignment, SerialisableType
cogent3	fast_slow_dist	True	Pairwise distance calculation for aligned sequences.	Alignment, ArrayAlignment	DistanceMatrix, SerialisableType
cogent3	fixed_length	True	Sample an alignment to a fixed length.	Alignment, ArrayAlignment	Alignment, ArrayAlignment, SerialisableType
cogent3	gap_dist	True	compute the pairwise difference in gaps using affine gap score	Alignment, ArrayAlignment	DistanceMatrix
cogent3	hypothesis	True	Specify a hypothesis through defining two models.	Alignment, ArrayAlignment	SerialisableType, hypothesis_result, model_collection_result
cogent3	ic_score	True	compute the Information Content alignment quality score	Alignment, ArrayAlignment	float
cogent3	jaccard_dist	True	Calculates the pairwise Jaccard distance between the sets of kmers generated from sequences in the collection. A measure of distance for unaligned sequences.	SequenceCollection	DistanceMatrix
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
cogent3	min_length	True	Filters sequence collections / alignments by length.	Alignment, ArrayAlignment, SequenceCollection	Alignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3	model	True	Define a substitution model + tree for maximum likelihood evaluation.	Alignment, ArrayAlignment	SerialisableType, model_result
cogent3	model_collection	True	Fits a collection of models.	Alignment, ArrayAlignment	SerialisableType, hypothesis_result, model_collection_result
cogent3	natsel_neutral	True	Test of selective neutrality by assessing whether omega equals 1. Under the alternate, there is one omega for all branches and all sites.	Alignment, ArrayAlignment	SerialisableType, hypothesis_result
cogent3	natsel_sitehet	True	Test for site-heterogeneity in omega. Under null, there are 2 site-classes, omega < 1 and omega = 1. Under the alternate, an additional site-class of omega > 1 is added.	Alignment, ArrayAlignment	SerialisableType, hypothesis_result
cogent3	natsel_timehet	True	The branch heterogeneity hypothesis test for natural selection. Tests for whether a single omega for all branches is sufficient against the alternate that a user specified subset of branches has a distinct value (or values) of omega.	Alignment, ArrayAlignment	SerialisableType, hypothesis_result
cogent3	natsel_zhang	True	The branch by site-class hypothesis test for natural selection of Zhang et al MBE 22: 2472-2479.	Alignment, ArrayAlignment	SerialisableType, hypothesis_result
cogent3	omit_bad_seqs	True	Eliminates sequences from Alignment based on gap fraction, unique gaps.	Alignment, ArrayAlignment	Alignment, ArrayAlignment, SerialisableType
cogent3	omit_degenerates	True	Excludes alignment columns with degenerate characters. Can accomodate reading frame.	Alignment, ArrayAlignment	Alignment, ArrayAlignment, SerialisableType
cogent3	omit_duplicated	True	Removes redundant sequences, recording dropped sequences in seqs.info.dropped.	Alignment, ArrayAlignment, SequenceCollection	Alignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3	omit_gap_pos	True	Excludes gapped alignment columns meeting a threshold. Can accomodate reading frame.	Alignment, ArrayAlignment	Alignment, ArrayAlignment, SerialisableType
cogent3	progressive_align	True	Progressive multiple sequence alignment via any cogent3 model.	SequenceCollection	Alignment, ArrayAlignment, SerialisableType
cogent3	quick_tree	True	Computes a Neighbour Joining tree from pairwise distances.	DistanceMatrix	PhyloNode, SerialisableType, TreeNode
cogent3	scale_branches	True	Transforms tree branch lengths from nucleotide to codon, or the converse. Returns a new tree with lengths divided by scalar	PhyloNode, TreeNode	PhyloNode, SerialisableType, TreeNode
cogent3	select_translatable	True	Selects translatable sequences by identifying the most likely reading frame. Sequences are truncated to modulo 3. seqs.info has a translation_errors entry.	Alignment, ArrayAlignment, SequenceCollection	Alignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3	smith_waterman	True	Local alignment of two sequences using the Smith-Waterman algorithm	SequenceCollection	Alignment, ArrayAlignment
cogent3	sp_score	True	Compute a variant of Sum of Pairs alignment quality score	Alignment, ArrayAlignment	float
cogent3	tabulate_stats	True	Extracts all model statistics from model_result as Table.	model_result	SerialisableType, tabular_result
cogent3	take_codon_positions	True	Extracts the specified codon position(s) from an alignment.	Alignment, ArrayAlignment	Alignment, ArrayAlignment, SerialisableType
cogent3	take_n_seqs	True	Selects n sequences from a collection. Chooses first n sequences, or selects randomly if specified.	Alignment, ArrayAlignment, SequenceCollection	Alignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3	take_named_seqs	True	Selects named sequences from a collection.	Alignment, ArrayAlignment, SequenceCollection	Alignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3	translate_seqs	True	Translates nucleic acid sequences into protein sequences, assumes in correct reading frame.	Alignment, ArrayAlignment, SequenceCollection	Alignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3	trim_stop_codons	True	Removes terminal stop codons.	Alignment, ArrayAlignment, SequenceCollection	Alignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3	uniformize_tree	True	Standardises the orientation of unrooted trees.	PhyloNode, TreeNode	PhyloNode, SerialisableType, TreeNode
cogent3	write_db	True	Write serialised objects to a database instance.	SerialisableType	IdentifierType
cogent3	write_json	True	Writes data in json format.	SerialisableType	IdentifierType
cogent3	write_seqs	True	Write sequences in standard formats.	Alignment, ArrayAlignment, SequenceCollection	IdentifierType
cogent3	write_tabular	True	Writes tabular data in text format supported by the cogent3 Table object.	DictArray, DistanceMatrix, Table	IdentifierType

46 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.