Index _ | A | B | C | D | F | G | H | I | K | L | M | N | P | Q | R | S | T | V _ __init__() (abutils.tl.PairwiseAlignment method) A abutils.utils.decorators module abutils.utils.progbar module abutils.utils.s3 module aln_string (abutils.tl.MultipleSequenceAlignment property) annotations (abutils.core.sequence.Sequence property) as_fasta() (abutils.core.sequence.Sequence method) assign_pairs() (in module abutils.core.pair) B bar() (in module abutils.plots) C centroid (abutils.tl.Cluster attribute) centroids (abutils.tl.Clusters attribute) cigar (abutils.tl.PairwiseAlignment property) clonify() (in module abutils.tools) Cluster (class in abutils.tl) cluster() (abutils.tools.phylo.Phylogeny method) (in module abutils.tl) clusters (abutils.tl.Clusters attribute) Clusters (class in abutils.tl) codon_optimize() (abutils.core.sequence.Sequence method) concatenate_files() (in module abutils.io) consensus (abutils.tl.Cluster attribute) count (abutils.tl.Clusters attribute) D donut() (in module abutils.core.lineage) (in module abutils.plots) F famsa() (in module abutils.tl) fasta (abutils.core.sequence.Sequence property) fastq (abutils.core.sequence.Sequence property) fasttree() (in module abutils.tools.phylo) format() (abutils.tl.MultipleSequenceAlignment method) from_pandas() (in module abutils.io) from_polars() (in module abutils.io) G get() (abutils.core.sequence.Sequence method) get_cmap() (in module abutils.cl) global_alignment() (in module abutils.tl) GlobalAlignment (class in abutils.tl) group_lineages() (in module abutils.core.lineage) H hex_to_rgb() (in module abutils.cl) hls() (in module abutils.cl) husl() (in module abutils.cl) I igphyml() (in module abutils.utils.phylogeny) K kde() (in module abutils.plots) keys() (abutils.core.sequence.Sequence method) L largest_cluster (abutils.tl.Clusters attribute) Lineage (class in abutils.core.lineage) list_files() (in module abutils.io) (in module abutils.utils.pipeline) local_alignment() (in module abutils.tl) LocalAlignment (class in abutils.tl) lsd() (in module abutils.utils.phylogeny) M mafft() (in module abutils.tl) make_consensus() (abutils.tl.Cluster method) (abutils.tl.MultipleSequenceAlignment method) make_dir() (in module abutils.io) (in module abutils.utils.pipeline) module abutils.utils.decorators abutils.utils.progbar abutils.utils.s3 monitor_celery_jobs() (in module abutils) monitor_mp_jobs() (in module abutils) monochrome_palette() (in module abutils.cl) MultipleSequenceAlignment (class in abutils.tl) muscle() (in module abutils.tl) N name (abutils.tl.Cluster attribute) P Pair (class in abutils.core.pair) PairwiseAlignment (class in abutils.tl) palettes (in module abutils.cl) parse_fasta() (in module abutils.io) parse_fastq() (in module abutils.io) parse_fastx() (in module abutils.io) Phylogeny (class in abutils.tools.phylo) phylogeny() (abutils.core.lineage.Lineage method) (in module abutils.tools.phylo) plot() (abutils.tools.phylo.Phylogeny method) progress_bar() (in module abutils) Q query (abutils.tl.PairwiseAlignment attribute) R raw_query (abutils.tl.PairwiseAlignment attribute) raw_target (abutils.tl.PairwiseAlignment attribute) read_airr() (in module abutils.io) read_csv() (in module abutils.io) read_fasta() (in module abutils.io) read_fastq() (in module abutils.io) read_fastx() (in module abutils.io) read_parquet() (in module abutils.io) region() (abutils.core.sequence.Sequence method) rename_file() (in module abutils.io) reverse_complement (abutils.core.sequence.Sequence property) reverse_complement() (in module abutils.core.sequence) rgb_to_hex() (in module abutils.cl) root (abutils.tools.phylo.Phylogeny property) S scatter() (in module abutils.plots) semiglobal_alignment() (in module abutils.tl) SemiGlobalAlignment (class in abutils.tl) seq_ids (abutils.tl.Cluster attribute) Sequence (class in abutils.core.sequence) sequences (abutils.tl.Cluster attribute) (abutils.tl.MultipleSequenceAlignment property) show_palettes() (in module abutils.cl) size (abutils.tl.Cluster attribute) sizes (abutils.tools.phylo.Phylogeny property) split_fasta() (in module abutils.io) split_fastq() (in module abutils.io) split_fastx() (in module abutils.io) split_parquet() (in module abutils.io) T target (abutils.tl.PairwiseAlignment attribute) target_id (abutils.tl.PairwiseAlignment attribute) (abutils.tl.PairwiseAlignment property) to_airr() (in module abutils.io) to_csv() (in module abutils.io) to_fasta() (in module abutils.io) to_fastq() (in module abutils.io) to_pandas() (in module abutils.io) to_parquet() (in module abutils.io) to_polars() (in module abutils.io) translate() (abutils.core.sequence.Sequence method) (in module abutils.core.sequence) tree (abutils.tools.phylo.Phylogeny property) true_false_palette (in module abutils.cl) truncate_colormap() (in module abutils.cl) V values() (abutils.core.sequence.Sequence method)