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()
module | name | composable | doc | input type | output type |
---|---|---|---|---|---|
cogent3.app.align | align_to_ref | True | Aligns sequences to a nominated reference in the unaligned collection. | SequenceCollection | Alignment, ArrayAlignment, SerialisableType |
cogent3.app.evo | ancestral_states | True | Computes ancestral state probabilities from a model result. | model_result | SerialisableType, tabular_result |
cogent3.app.dist | approx_jc69 | True | Converts p-distances and returns pairwise JC69 distances | DistanceMatrix | DistanceMatrix |
cogent3.app.dist | approx_pdist | True | Calculates an approximation of the p-distance between sequences based on Jaccard distances (see Notes for details). | DistanceMatrix | DistanceMatrix |
cogent3.app.evo | bootstrap | True | Parametric bootstrap for a provided hypothesis. | Alignment, ArrayAlignment | SerialisableType, bootstrap_result |
cogent3.app.align | cogent3_score | True | returns the cogent3 log-likelihood as an alignment quality score | Alignment, ArrayAlignment | float |
cogent3.app.sample | concat | False | Creates a concatenated alignment from a series. | Alignment, ArrayAlignment | Alignment, ArrayAlignment, SerialisableType |
cogent3.app.dist | fast_slow_dist | True | Pairwise distance calculation for aligned sequences. | Alignment, ArrayAlignment | DistanceMatrix, SerialisableType |
cogent3.app.sample | fixed_length | True | Sample an alignment to a fixed length. | Alignment, ArrayAlignment | Alignment, ArrayAlignment, SerialisableType |
cogent3.app.dist | gap_dist | True | compute the pairwise difference in gaps using affine gap score | Alignment, ArrayAlignment | DistanceMatrix |
cogent3.app.evo | hypothesis | True | Specify a hypothesis through defining two models. | Alignment, ArrayAlignment | SerialisableType, hypothesis_result, model_collection_result |
cogent3.app.align | ic_score | True | compute the Information Content alignment quality score | Alignment, ArrayAlignment | float |
cogent3.app.dist | 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.app.io | load_aligned | True | Loads aligned sequences. Returns an Alignment object. | IdentifierType | Alignment, ArrayAlignment, SerialisableType |
cogent3.app.io | load_db | True | Loads serialised cogent3 objects from a db. Returns whatever object type was stored. | IdentifierType | SerialisableType |
cogent3.app.io | load_json | True | Loads json serialised cogent3 objects from a json file. Returns whatever object type was stored. | IdentifierType | SerialisableType |
cogent3.app.io | load_tabular | True | Loads delimited data. Returns a Table. | IdentifierType | DictArray, DistanceMatrix, Table |
cogent3.app.io | load_unaligned | True | Loads unaligned sequences. Returns a SequenceCollection. | IdentifierType | SequenceCollection, SerialisableType |
cogent3.app.sample | min_length | True | Filters sequence collections / alignments by length. | Alignment, ArrayAlignment, SequenceCollection | Alignment, ArrayAlignment, SequenceCollection, SerialisableType |
cogent3.app.evo | model | True | Define a substitution model + tree for maximum likelihood evaluation. | Alignment, ArrayAlignment | SerialisableType, model_result |
cogent3.app.evo | model_collection | True | Fits a collection of models. | Alignment, ArrayAlignment | SerialisableType, hypothesis_result, model_collection_result |
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. | Alignment, ArrayAlignment | SerialisableType, hypothesis_result |
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. | Alignment, ArrayAlignment | SerialisableType, hypothesis_result |
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 has a distinct value (or values) of omega. | Alignment, ArrayAlignment | SerialisableType, hypothesis_result |
cogent3.app.evo | 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.app.sample | omit_bad_seqs | True | Eliminates sequences from Alignment based on gap fraction, unique gaps. | Alignment, ArrayAlignment | Alignment, ArrayAlignment, SerialisableType |
cogent3.app.sample | omit_degenerates | True | Excludes alignment columns with degenerate characters. Can accomodate reading frame. | Alignment, ArrayAlignment | Alignment, ArrayAlignment, SerialisableType |
cogent3.app.sample | omit_duplicated | True | Removes redundant sequences, recording dropped sequences in seqs.info.dropped. | Alignment, ArrayAlignment, SequenceCollection | Alignment, ArrayAlignment, SequenceCollection, SerialisableType |
cogent3.app.sample | omit_gap_pos | True | Excludes gapped alignment columns meeting a threshold. Can accomodate reading frame. | Alignment, ArrayAlignment | Alignment, ArrayAlignment, SerialisableType |
cogent3.app.align | progressive_align | True | Progressive multiple sequence alignment via any cogent3 model. | SequenceCollection | Alignment, ArrayAlignment, SerialisableType |
cogent3.app.tree | quick_tree | True | Computes a Neighbour Joining tree from pairwise distances. | DistanceMatrix | PhyloNode, SerialisableType, TreeNode |
cogent3.app.tree | 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.app.translate | 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.app.align | smith_waterman | True | Local alignment of two sequences using the Smith-Waterman algorithm | SequenceCollection | Alignment, ArrayAlignment |
cogent3.app.align | sp_score | True | Compute a variant of Sum of Pairs alignment quality score | Alignment, ArrayAlignment | float |
cogent3.app.evo | tabulate_stats | True | Extracts all model statistics from model_result as Table. | model_result | SerialisableType, tabular_result |
cogent3.app.sample | take_codon_positions | True | Extracts the specified codon position(s) from an alignment. | Alignment, ArrayAlignment | Alignment, ArrayAlignment, SerialisableType |
cogent3.app.sample | 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.app.sample | take_named_seqs | True | Selects named sequences from a collection. | Alignment, ArrayAlignment, SequenceCollection | Alignment, ArrayAlignment, SequenceCollection, SerialisableType |
cogent3.app.translate | translate_seqs | True | Translates nucleic acid sequences into protein sequences, assumes in correct reading frame. | Alignment, ArrayAlignment, SequenceCollection | Alignment, ArrayAlignment, SequenceCollection, SerialisableType |
cogent3.app.sample | trim_stop_codons | True | Removes terminal stop codons. | Alignment, ArrayAlignment, SequenceCollection | Alignment, ArrayAlignment, SequenceCollection, SerialisableType |
cogent3.app.tree | uniformize_tree | True | Standardises the orientation of unrooted trees. | PhyloNode, TreeNode | PhyloNode, SerialisableType, TreeNode |
cogent3.app.io | write_db | True | Write serialised objects to a database instance. | SerialisableType | IdentifierType |
cogent3.app.io | write_json | True | Writes data in json format. | SerialisableType | IdentifierType |
cogent3.app.io | write_seqs | True | Write sequences in standard formats. | Alignment, ArrayAlignment, SequenceCollection | IdentifierType |
cogent3.app.io | 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")
module | name | composable | doc | input type | output type |
---|---|---|---|---|---|
cogent3.app.io | load_aligned | True | Loads aligned sequences. Returns an Alignment object. | IdentifierType | Alignment, ArrayAlignment, SerialisableType |
cogent3.app.io | load_db | True | Loads serialised cogent3 objects from a db. Returns whatever object type was stored. | IdentifierType | SerialisableType |
cogent3.app.io | load_json | True | Loads json serialised cogent3 objects from a json file. Returns whatever object type was stored. | IdentifierType | SerialisableType |
cogent3.app.io | load_tabular | True | Loads delimited data. Returns a Table. | IdentifierType | DictArray, DistanceMatrix, Table |
cogent3.app.io | load_unaligned | True | Loads unaligned sequences. Returns a SequenceCollection. | IdentifierType | SequenceCollection, SerialisableType |
5 rows x 6 columns