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()
modulenamecomposabledocinput typeoutput type
cogent3.app.alignalign_to_refTrueAligns sequences to a nominated reference in the unaligned collection.SequenceCollectionAlignment, ArrayAlignment, SerialisableType
cogent3.app.evoancestral_statesTrueComputes ancestral state probabilities from a model result.model_resultSerialisableType, tabular_result
cogent3.app.distapprox_jc69TrueConverts p-distances and returns pairwise JC69 distancesDistanceMatrixDistanceMatrix
cogent3.app.distapprox_pdistTrueCalculates an approximation of the p-distance between sequences based on Jaccard distances (see Notes for details).DistanceMatrixDistanceMatrix
cogent3.app.evobootstrapTrueParametric bootstrap for a provided hypothesis.Alignment, ArrayAlignmentSerialisableType, bootstrap_result
cogent3.app.aligncogent3_scoreTruereturns the cogent3 log-likelihood as an alignment quality scoreAlignment, ArrayAlignmentfloat
cogent3.app.sampleconcatFalseCreates a concatenated alignment from a series.Alignment, ArrayAlignmentAlignment, ArrayAlignment, SerialisableType
cogent3.app.distfast_slow_distTruePairwise distance calculation for aligned sequences.Alignment, ArrayAlignmentDistanceMatrix, SerialisableType
cogent3.app.samplefixed_lengthTrueSample an alignment to a fixed length.Alignment, ArrayAlignmentAlignment, ArrayAlignment, SerialisableType
cogent3.app.distgap_distTruecompute the pairwise difference in gaps using affine gap scoreAlignment, ArrayAlignmentDistanceMatrix
cogent3.app.evohypothesisTrueSpecify a hypothesis through defining two models.Alignment, ArrayAlignmentSerialisableType, hypothesis_result, model_collection_result
cogent3.app.alignic_scoreTruecompute the Information Content alignment quality scoreAlignment, ArrayAlignmentfloat
cogent3.app.distjaccard_distTrueCalculates the pairwise Jaccard distance between the sets of kmers generated from sequences in the collection. A measure of distance for unaligned sequences.SequenceCollectionDistanceMatrix
cogent3.app.ioload_alignedTrueLoads aligned sequences. Returns an Alignment object.IdentifierTypeAlignment, ArrayAlignment, SerialisableType
cogent3.app.ioload_dbTrueLoads serialised cogent3 objects from a db. Returns whatever object type was stored.IdentifierTypeSerialisableType
cogent3.app.ioload_jsonTrueLoads json serialised cogent3 objects from a json file. Returns whatever object type was stored.IdentifierTypeSerialisableType
cogent3.app.ioload_tabularTrueLoads delimited data. Returns a Table.IdentifierTypeDictArray, DistanceMatrix, Table
cogent3.app.ioload_unalignedTrueLoads unaligned sequences. Returns a SequenceCollection.IdentifierTypeSequenceCollection, SerialisableType
cogent3.app.samplemin_lengthTrueFilters sequence collections / alignments by length.Alignment, ArrayAlignment, SequenceCollectionAlignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3.app.evomodelTrueDefine a substitution model + tree for maximum likelihood evaluation.Alignment, ArrayAlignmentSerialisableType, model_result
cogent3.app.evomodel_collectionTrueFits a collection of models.Alignment, ArrayAlignmentSerialisableType, hypothesis_result, model_collection_result
cogent3.app.evonatsel_neutralTrueTest of selective neutrality by assessing whether omega equals 1. Under the alternate, there is one omega for all branches and all sites.Alignment, ArrayAlignmentSerialisableType, hypothesis_result
cogent3.app.evonatsel_sitehetTrueTest 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, ArrayAlignmentSerialisableType, hypothesis_result
cogent3.app.evonatsel_timehetTrueThe 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, ArrayAlignmentSerialisableType, hypothesis_result
cogent3.app.evonatsel_zhangTrueThe branch by site-class hypothesis test for natural selection of Zhang et al MBE 22: 2472-2479.Alignment, ArrayAlignmentSerialisableType, hypothesis_result
cogent3.app.sampleomit_bad_seqsTrueEliminates sequences from Alignment based on gap fraction, unique gaps.Alignment, ArrayAlignmentAlignment, ArrayAlignment, SerialisableType
cogent3.app.sampleomit_degeneratesTrueExcludes alignment columns with degenerate characters. Can accomodate reading frame.Alignment, ArrayAlignmentAlignment, ArrayAlignment, SerialisableType
cogent3.app.sampleomit_duplicatedTrueRemoves redundant sequences, recording dropped sequences in seqs.info.dropped.Alignment, ArrayAlignment, SequenceCollectionAlignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3.app.sampleomit_gap_posTrueExcludes gapped alignment columns meeting a threshold. Can accomodate reading frame.Alignment, ArrayAlignmentAlignment, ArrayAlignment, SerialisableType
cogent3.app.alignprogressive_alignTrueProgressive multiple sequence alignment via any cogent3 model.SequenceCollectionAlignment, ArrayAlignment, SerialisableType
cogent3.app.treequick_treeTrueComputes a Neighbour Joining tree from pairwise distances.DistanceMatrixPhyloNode, SerialisableType, TreeNode
cogent3.app.treescale_branchesTrueTransforms tree branch lengths from nucleotide to codon, or the converse. Returns a new tree with lengths divided by scalarPhyloNode, TreeNodePhyloNode, SerialisableType, TreeNode
cogent3.app.translateselect_translatableTrueSelects translatable sequences by identifying the most likely reading frame. Sequences are truncated to modulo 3. seqs.info has a translation_errors entry.Alignment, ArrayAlignment, SequenceCollectionAlignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3.app.alignsmith_watermanTrueLocal alignment of two sequences using the Smith-Waterman algorithmSequenceCollectionAlignment, ArrayAlignment
cogent3.app.alignsp_scoreTrueCompute a variant of Sum of Pairs alignment quality scoreAlignment, ArrayAlignmentfloat
cogent3.app.evotabulate_statsTrueExtracts all model statistics from model_result as Table.model_resultSerialisableType, tabular_result
cogent3.app.sampletake_codon_positionsTrueExtracts the specified codon position(s) from an alignment.Alignment, ArrayAlignmentAlignment, ArrayAlignment, SerialisableType
cogent3.app.sampletake_n_seqsTrueSelects n sequences from a collection. Chooses first n sequences, or selects randomly if specified.Alignment, ArrayAlignment, SequenceCollectionAlignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3.app.sampletake_named_seqsTrueSelects named sequences from a collection.Alignment, ArrayAlignment, SequenceCollectionAlignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3.app.translatetranslate_seqsTrueTranslates nucleic acid sequences into protein sequences, assumes in correct reading frame.Alignment, ArrayAlignment, SequenceCollectionAlignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3.app.sampletrim_stop_codonsTrueRemoves terminal stop codons.Alignment, ArrayAlignment, SequenceCollectionAlignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3.app.treeuniformize_treeTrueStandardises the orientation of unrooted trees.PhyloNode, TreeNodePhyloNode, SerialisableType, TreeNode
cogent3.app.iowrite_dbTrueWrite serialised objects to a database instance.SerialisableTypeIdentifierType
cogent3.app.iowrite_jsonTrueWrites data in json format.SerialisableTypeIdentifierType
cogent3.app.iowrite_seqsTrueWrite sequences in standard formats.Alignment, ArrayAlignment, SequenceCollectionIdentifierType
cogent3.app.iowrite_tabularTrueWrites tabular data in text format supported by the cogent3 Table object.DictArray, DistanceMatrix, TableIdentifierType

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")
modulenamecomposabledocinput typeoutput type
cogent3.app.ioload_alignedTrueLoads aligned sequences. Returns an Alignment object.IdentifierTypeAlignment, ArrayAlignment, SerialisableType
cogent3.app.ioload_dbTrueLoads serialised cogent3 objects from a db. Returns whatever object type was stored.IdentifierTypeSerialisableType
cogent3.app.ioload_jsonTrueLoads json serialised cogent3 objects from a json file. Returns whatever object type was stored.IdentifierTypeSerialisableType
cogent3.app.ioload_tabularTrueLoads delimited data. Returns a Table.IdentifierTypeDictArray, DistanceMatrix, Table
cogent3.app.ioload_unalignedTrueLoads unaligned sequences. Returns a SequenceCollection.IdentifierTypeSequenceCollection, SerialisableType

5 rows x 6 columns