What apps are there?

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).

Apps that are identified as “composable” (with a value of True under that clumn) can be combined into a single function by addition.

from cogent3 import available_apps

available_apps()

module	name	composable	doc	inputs	outputs	data type
cogent3.app.align	align_to_ref	True	Aligns to a reference seq, no gaps in the reference. Returns an Alignment object.	sequences	aligned, serialisable	SequenceCollection
cogent3.app.align	progressive_align	True	Progressive multiple sequence alignment via any cogent3 model. Returns an Alignment object.	sequences	aligned, serialisable	SequenceCollection
cogent3.app.dist	fast_slow_dist	True	Pairwise distance calculation. Uses fast (but less numerically robust) approach where possible, slow (robust) approach when not. Returns a DistanceMatrix.	aligned	pairwise_distances, serialisable	ArrayAlignment, Alignment
cogent3.app.evo	ancestral_states	True	Computes ancestral state probabilities from a model result. Returns a dict with a DictArray for each node.	model_result	result, tabular_result, serialisable	model_result
cogent3.app.evo	bootstrap	True	Parametric bootstrap for a provided hypothesis. Returns a bootstrap_result.	aligned	result, bootstrap_result, serialisable	ArrayAlignment, Alignment
cogent3.app.evo	hypothesis	True	Specify a hypothesis through defining two models. Returns a hypothesis_result.	aligned, serialisable	result, hypothesis_result, serialisable	ArrayAlignment, Alignment
cogent3.app.evo	model	True	Define a substitution model + tree for maximum likelihood evaluation. Returns model_result.	aligned, serialisable	result, model_result, serialisable	ArrayAlignment, Alignment
cogent3.app.evo	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.	aligned, serialisable	result, hypothesis_result, serialisable	ArrayAlignment, Alignment
cogent3.app.evo	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.	aligned, serialisable	result, hypothesis_result, serialisable	ArrayAlignment, Alignment
cogent3.app.evo	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 have a distinct value (or values) of omega.	aligned, serialisable	result, hypothesis_result, serialisable	ArrayAlignment, Alignment
cogent3.app.evo	natsel_zhang	True	The branch by site-class hypothesis test for natural selection of Zhang et al MBE 22: 2472-2479. Note: Our implementation is not as parametrically succinct as that of Zhang et al, we have 1 additional bin probability.	aligned, serialisable	result, hypothesis_result, serialisable	ArrayAlignment, Alignment
cogent3.app.evo	tabulate_stats	True	Extracts all model statistics from model_result as Table.	model_result, serialisable	result, tabular_result, serialisable	model_result
cogent3.app.io	load_aligned	True	Loads aligned sequences. Returns an Alignment object.		aligned, serialisable	DataStoreMember, str, Path
cogent3.app.io	load_db	True	Loads json serialised cogent3 objects from a TinyDB file. Returns whatever object type was stored.		serialisable
cogent3.app.io	load_json	True	Loads json serialised cogent3 objects from a json file. Returns whatever object type was stored.		serialisable
cogent3.app.io	load_tabular	True	Loads delimited data. Returns a Table.		tabular, serialisable	DataStoreMember, str, Path
cogent3.app.io	load_unaligned	True	Loads unaligned sequences. Returns a SequenceCollection.		sequences, serialisable	DataStoreMember, str, Path
cogent3.app.io	write_db	True	Writes json serialised objects to a TinyDB instance.	serialisable	identifier, serialisable
cogent3.app.io	write_json	True	Writes json serialised objects to individual json files.	serialisable	identifier, serialisable
cogent3.app.io	write_seqs	True	Writes sequences to text files in standard format.	sequences, aligned	sequences, aligned, identifier	ArrayAlignment, Alignment, SequenceCollection
cogent3.app.io	write_tabular	True	writes tabular data	tabular_result, tabular	identifier	Table, DictArray, DistanceMatrix
cogent3.app.sample	concat	False	Creates a concatenated alignment from a series. Returns an Alignment.
cogent3.app.sample	fixed_length	True	Sample an alignment to a fixed length. Returns an Alignment of the specified length, or NotCompleted if alignment too short.	aligned, serialisable	aligned, serialisable	ArrayAlignment, Alignment
cogent3.app.sample	min_length	True	Filters sequence collections / alignments by length. Returns the data if it satisfies the condition, NotCompleted otherwise.	sequences, aligned, serialisable	sequences, aligned, serialisable	ArrayAlignment, Alignment, SequenceCollection
cogent3.app.sample	omit_bad_seqs	True	Eliminates sequences from Alignment based on gap fraction, unique gaps. Returns modified alignment.	aligned, serialisable	aligned, serialisable	ArrayAlignment, Alignment
cogent3.app.sample	omit_degenerates	True	Excludes alignment columns with degenerate conditions. Can accomodate reading frame. Returns modified Alignment.	aligned, serialisable	aligned, serialisable	ArrayAlignment, Alignment
cogent3.app.sample	omit_duplicated	True	Removes redundant sequences, recording dropped sequences in seqs.info.dropped. Returns sequence collection with only unique sequences.	sequences, serialisable, aligned	sequences, serialisable, aligned	ArrayAlignment, Alignment, SequenceCollection
cogent3.app.sample	omit_gap_pos	True	Excludes gapped alignment columns meeting a threshold. Can accomodate reading frame. Returns modified Alignment.	aligned, serialisable	aligned, serialisable	ArrayAlignment, Alignment
cogent3.app.sample	take_codon_positions	True	Extracts the specified codon position(s) from an alignment. Returns an Alignment.	aligned, serialisable	aligned, serialisable	ArrayAlignment, Alignment
cogent3.app.sample	take_named_seqs	True	Extracts (or everything but) named sequences. Returns a filtered sequences, alignment that satisified the condition, NotCompleted otherwise.	sequences, aligned, serialisable	sequences, aligned, serialisable	ArrayAlignment, Alignment, SequenceCollection
cogent3.app.sample	trim_stop_codons	True	Removes terminal stop codons. Returns sequences / alignment.	sequences, aligned, serialisable	sequences, aligned, serialisable	ArrayAlignment, Alignment, SequenceCollection
cogent3.app.translate	select_translatable	True	Identifies most likely reading frame. Returns modified sequences / alignment, if it could be resolved, NotCompleted otherwise.	sequences, aligned	sequences	ArrayAlignment, Alignment, SequenceCollection
cogent3.app.translate	translate_seqs	True	Translates sequences, assumes in correct reading frame.	sequences, aligned	sequences, aligned	ArrayAlignment, Alignment, SequenceCollection
cogent3.app.tree	quick_tree	True	Neighbour Joining tree based on pairwise distances.	pairwise_distances	tree, serialisable	DistanceMatrix
cogent3.app.tree	scale_branches	True	Transforms tree branch lengths from nucleotide to codon, or the converse. Returns a Tree.	tree	tree, serialisable	PhyloNode, TreeNode
cogent3.app.tree	uniformize_tree	True	Standardises the orientation of unrooted trees. Returns a Tree.	tree	tree, serialisable	PhyloNode, TreeNode
cogent3.app.composable	user_function	True	wrapper class for user specified function

37 rows x 7 columns