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()
modulenamecomposabledocinputsoutputsdata type
cogent3.app.alignalign_to_refTrueAligns to a reference seq, no gaps in the reference. Returns an Alignment object.sequencesaligned, serialisableSequenceCollection
cogent3.app.alignprogressive_alignTrueProgressive multiple sequence alignment via any cogent3 model. Returns an Alignment object.sequencesaligned, serialisableSequenceCollection
cogent3.app.distfast_slow_distTruePairwise distance calculation for aligned sequences. Uses fast (but less numerically robust) approach where possible, slow (robust) approach when not. Returns a DistanceMatrix. alignedpairwise_distances, serialisableArrayAlignment, Alignment
cogent3.app.evoancestral_statesTrueComputes ancestral state probabilities from a model result. Returns a dict with a DictArray for each node.model_resultresult, tabular_result, serialisablemodel_result
cogent3.app.evobootstrapTrueParametric bootstrap for a provided hypothesis. Returns a bootstrap_result.alignedresult, bootstrap_result, serialisableArrayAlignment, Alignment
cogent3.app.evohypothesisTrueSpecify a hypothesis through defining two models. Returns a hypothesis_result.aligned, serialisableresult, hypothesis_result, serialisableArrayAlignment, Alignment
cogent3.app.evomodelTrueDefine a substitution model + tree for maximum likelihood evaluation. Returns model_result.aligned, serialisableresult, model_result, serialisableArrayAlignment, Alignment
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. aligned, serialisableresult, hypothesis_result, serialisableArrayAlignment, Alignment
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.aligned, serialisableresult, hypothesis_result, serialisableArrayAlignment, Alignment
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 have a distinct value (or values) of omega. aligned, serialisableresult, hypothesis_result, serialisableArrayAlignment, Alignment
cogent3.app.evonatsel_zhangTrueThe 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, serialisableresult, hypothesis_result, serialisableArrayAlignment, Alignment
cogent3.app.evotabulate_statsTrueExtracts all model statistics from model_result as Table.model_result, serialisableresult, tabular_result, serialisablemodel_result
cogent3.app.ioload_alignedTrueLoads aligned sequences. Returns an Alignment object.aligned, serialisableDataStoreMember, str, Path
cogent3.app.ioload_dbTrueLoads json serialised cogent3 objects from a TinyDB file. Returns whatever object type was stored.serialisable
cogent3.app.ioload_jsonTrueLoads json serialised cogent3 objects from a json file. Returns whatever object type was stored.serialisable
cogent3.app.ioload_tabularTrueLoads delimited data. Returns a Table.tabular, serialisableDataStoreMember, str, Path
cogent3.app.ioload_unalignedTrueLoads unaligned sequences. Returns a SequenceCollection.sequences, serialisableDataStoreMember, str, Path
cogent3.app.iowrite_dbTrueWrites json serialised objects to a TinyDB instance.serialisableidentifier, serialisable
cogent3.app.iowrite_jsonTrueWrites json serialised objects to individual json files.serialisableidentifier, serialisable
cogent3.app.iowrite_seqsTrueWrites sequences to text files in standard format.sequences, alignedsequences, aligned, identifierArrayAlignment, Alignment, SequenceCollection
cogent3.app.iowrite_tabularTruewrites tabular datatabular_result, tabularidentifierTable, DictArray, DistanceMatrix
cogent3.app.sampleconcatFalseCreates a concatenated alignment from a series. Returns an Alignment.
cogent3.app.samplefixed_lengthTrueSample an alignment to a fixed length. Returns an Alignment of the specified length, or NotCompleted if alignment too short.aligned, serialisablealigned, serialisableArrayAlignment, Alignment
cogent3.app.samplemin_lengthTrueFilters sequence collections / alignments by length. Returns the data if it satisfies the condition, NotCompleted otherwise.sequences, aligned, serialisablesequences, aligned, serialisableArrayAlignment, Alignment, SequenceCollection
cogent3.app.sampleomit_bad_seqsTrueEliminates sequences from Alignment based on gap fraction, unique gaps. Returns modified alignment.aligned, serialisablealigned, serialisableArrayAlignment, Alignment
cogent3.app.sampleomit_degeneratesTrueExcludes alignment columns with degenerate conditions. Can accomodate reading frame. Returns modified Alignment.aligned, serialisablealigned, serialisableArrayAlignment, Alignment
cogent3.app.sampleomit_duplicatedTrueRemoves redundant sequences, recording dropped sequences in seqs.info.dropped. Returns sequence collection with only unique sequences.sequences, serialisable, alignedsequences, serialisable, alignedArrayAlignment, Alignment, SequenceCollection
cogent3.app.sampleomit_gap_posTrueExcludes gapped alignment columns meeting a threshold. Can accomodate reading frame. Returns modified Alignment.aligned, serialisablealigned, serialisableArrayAlignment, Alignment
cogent3.app.sampletake_codon_positionsTrueExtracts the specified codon position(s) from an alignment. Returns an Alignment.aligned, serialisablealigned, serialisableArrayAlignment, Alignment
cogent3.app.sampletake_n_seqsTrueSelects n sequences from a collection. Chooses first n sequences, or selects randomly if specified. Returns original object type with the selected sequences, NotCompleted object otherwise. sequences, aligned, serialisablesequences, aligned, serialisableArrayAlignment, Alignment, SequenceCollection
cogent3.app.sampletake_named_seqsTrueExtracts (or everything but) named sequences. Returns a filtered sequences, alignment that satisified the condition, NotCompleted otherwise.sequences, aligned, serialisablesequences, aligned, serialisableArrayAlignment, Alignment, SequenceCollection
cogent3.app.sampletrim_stop_codonsTrueRemoves terminal stop codons. Returns sequences / alignment.sequences, aligned, serialisablesequences, aligned, serialisableArrayAlignment, Alignment, SequenceCollection
cogent3.app.translateselect_translatableTrueIdentifies most likely reading frame. Returns modified sequences / alignment, if it could be resolved, NotCompleted otherwise.sequences, alignedsequencesArrayAlignment, Alignment, SequenceCollection
cogent3.app.translatetranslate_seqsTrueTranslates sequences, assumes in correct reading frame.sequences, alignedsequences, alignedArrayAlignment, Alignment, SequenceCollection
cogent3.app.treequick_treeTrueNeighbour Joining tree based on pairwise distances.pairwise_distancestree, serialisableDistanceMatrix
cogent3.app.treescale_branchesTrueTransforms tree branch lengths from nucleotide to codon, or the converse. Returns a Tree.treetree, serialisablePhyloNode, TreeNode
cogent3.app.treeuniformize_treeTrueStandardises the orientation of unrooted trees. Returns a Tree.treetree, serialisablePhyloNode, TreeNode
cogent3.app.composableuser_functionTruewrapper class for user specified function

38 rows x 7 columns