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 column) can be combined into a single function by addition.

from cogent3 import available_apps

available_apps()
modulenamecomposabledocinput typeoutput type
cogent3.app.distfast_slow_distTruePairwise distance calculation for aligned sequences.Alignment, ArrayAlignmentDistanceMatrix, SerialisableType
cogent3.app.treescale_branchesTrueTransforms tree branch lengths from nucleotide to codon, or the converse.PhyloNode, TreeNodePhyloNode, SerialisableType, TreeNode
cogent3.app.treeuniformize_treeTrueStandardises the orientation of unrooted trees.PhyloNode, TreeNodePhyloNode, SerialisableType, TreeNode
cogent3.app.treequick_treeTrueNeighbour Joining tree based on pairwise distances.DistanceMatrixPhyloNode, SerialisableType, TreeNode
cogent3.app.alignalign_to_refTrueAligns sequences to a nominated reference in the unaligned collection.SequenceCollectionAlignment, ArrayAlignment, SerialisableType
cogent3.app.alignprogressive_alignTrueProgressive multiple sequence alignment via any cogent3 model.SequenceCollectionAlignment, ArrayAlignment, 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.evohypothesisTrueSpecify a hypothesis through defining two models.Alignment, ArrayAlignmentSerialisableType, hypothesis_result, model_collection_result
cogent3.app.evobootstrapTrueParametric bootstrap for a provided hypothesis.Alignment, ArrayAlignmentSerialisableType, bootstrap_result
cogent3.app.evoancestral_statesTrueComputes ancestral state probabilities from a model result.model_resultSerialisableType, tabular_result
cogent3.app.evotabulate_statsTrueExtracts all model statistics from model_result as Table.model_resultSerialisableType, tabular_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_zhangTrueThe branch by site-class hypothesis test for natural selection of Zhang et al MBE 22: 2472-2479.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.ioload_alignedTrueLoads aligned sequences. Returns an Alignment object.IdentifierTypeAlignment, ArrayAlignment, SerialisableType
cogent3.app.ioload_unalignedTrueLoads unaligned sequences. Returns a SequenceCollection.IdentifierTypeSequenceCollection, SerialisableType
cogent3.app.ioload_tabularTrueLoads delimited data. Returns a Table.IdentifierTypeDictArray, DistanceMatrix, Table
cogent3.app.iowrite_tabularTruewrites tabular dataDictArray, DistanceMatrix, TableIdentifierType
cogent3.app.iowrite_seqsTrueWrites sequences to text files in standard format.Alignment, ArrayAlignment, SequenceCollectionIdentifierType
cogent3.app.ioload_jsonTrueLoads json serialised cogent3 objects from a json file. Returns whatever object type was stored.IdentifierTypeSerialisableType
cogent3.app.iowrite_jsonTrueWrites json serialised objects to individual json files.SerialisableTypeIdentifierType
cogent3.app.ioload_dbTrueLoads json serialised cogent3 objects from a TinyDB file. Returns whatever object type was stored.IdentifierTypeSerialisableType
cogent3.app.iowrite_dbTrueWrites json serialised objects to a TinyDB instance.SerialisableTypeIdentifierType, SerialisableType
cogent3.app.translateselect_translatableTrueIdentifies most likely reading frame.Alignment, ArrayAlignment, SequenceCollectionAlignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3.app.translatetranslate_seqsTrueTranslates sequences, assumes in correct reading frame.Alignment, ArrayAlignment, SequenceCollectionAlignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3.app.sampleconcatFalseCreates a concatenated alignment from a series.Alignment, ArrayAlignmentAlignment, ArrayAlignment, SerialisableType
cogent3.app.sampleomit_degeneratesTrueExcludes alignment columns with degenerate conditions. Can accomodate reading frame.Alignment, ArrayAlignmentAlignment, ArrayAlignment, SerialisableType
cogent3.app.sampleomit_gap_posTrueExcludes gapped alignment columns meeting a threshold. Can accomodate reading frame.Alignment, ArrayAlignmentAlignment, ArrayAlignment, SerialisableType
cogent3.app.sampletake_codon_positionsTrueExtracts the specified codon position(s) from an alignment.Alignment, ArrayAlignmentAlignment, ArrayAlignment, SerialisableType
cogent3.app.sampletake_named_seqsTrueExtracts named sequences.Alignment, ArrayAlignment, SequenceCollectionAlignment, ArrayAlignment, SequenceCollection, 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.samplemin_lengthTrueFilters sequence collections / alignments by length.Alignment, ArrayAlignment, SequenceCollectionAlignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3.app.samplefixed_lengthTrueSample an alignment to a fixed length.Alignment, ArrayAlignmentAlignment, ArrayAlignment, SerialisableType
cogent3.app.sampleomit_bad_seqsTrueEliminates sequences from Alignment based on gap fraction, unique gaps.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.sampletrim_stop_codonsTrueRemoves terminal stop codons.Alignment, ArrayAlignment, SequenceCollectionAlignment, ArrayAlignment, SequenceCollection, SerialisableType

38 rows x 6 columns