Index of all namespaces
Various bioinformatic general utility tools
Various sequence aligners by means of low level hackery...
Intended to include/contain various utilities for operating with and on sequence data. Originally this was all about working with (NCBI) Blast+, CMFINDER (and associated utils) and Infernal tools, but now may branch out to many others.
E embl-sto->nc-sto embl-to-nc entry-aln-sqs entry-file->blastdb entry-file-difference entry-file-difference-with-seqs entry-file-intersect entry-file-intersect-with-seqs entry-file-setop entry-file-union entry-file-union-with-seqs entry-range->fasta-file
Various bio sequence file format readers, writers, verifiers, and manipulators.
G gaisr-seq-set? gbank->fna gbank-loci-sane-loci gbanks->fnas gen-entry-file gen-entry-nv-file gen-name-seq gen-name-seq-pairs gen-nc-genome-fnas genbank-recs genbk2gtf get-csv-entry-info get-ent-as-csv-info get-entries get-gaisr-csv-info get-legacy-csv-info get-selection-fna get-sto-as-csv-info
Various scoring, filtering, of sequence data.
Various information theory computations, calculations and results as applied to bio sequences and alignments thereof. Includes entropy, joint entropy, conditional entropy, mutual information, conditional mi, et. al.
_adjust-one _str-em account-for-symmetry adjust-seqs-info aln-conditional-mutual-information aln-entropy aln-freqs-probs aln-joint-entropy aln-mutual-information aln-shannon-entropy bg-freqs bg-freqs-probs bp-stats degap-freqs degap-tuples seq-pairs&indices seq-pairs-bpfreqs seq-vi seqs-freqs-probs seqs-shannon-entropy
Various sequence transformation and generation functions.