📦 perl5.42.3-bioperl

B

• bp_aacomp(1)amino acid composition of protein sequences✨
• bp_bioflat_index(1)index sequence files using Bio::DB::Flat✨
• bp_biogetseq(1)sequence retrieval using OBDA registry✨
• bp_dbsplit(1)script to split an input set of database(s) into smaller pieces✨
• bp_extract_feature_seq(1)extract the corresponding sequence for a specified feature type✨
• bp_fastam9_to_table(1)turn FASTA -m 9 output into NCBI -m 9 tabular output✨
• bp_fetch(1)fetches sequences from bioperl indexed databases✨
• bp_filter_search(1)filters searchio results, outputting a tab delimited summary✨
• bp_find-blast-matches(1)extract DNA sequences based on BLAST hits✨
• bp_gccalc(1)GC content of nucleotide sequences✨
• bp_genbank2gff3(1)Genbank->gbrowse-friendly GFF3✨
• bp_index(1)indexes files for use by bp_fetch.pl✨
• bp_local_taxonomydb_query(1)query a local TaxonomyDB for species or taxonid✨
• bp_make_mrna_protein(1)Convert an input mRNA/cDNA sequence into protein✨
• bp_mask_by_search(1)mask sequence(s) based on its alignment results✨
• bp_mrtrans(1)implement a transformer of alignments from protein to mrna coordinates✨
• bp_mutate(1)randomly mutagenize a single protein or DNA sequence✨
• bp_nexus2nh(1)convert nexus format trees (from PAUP* and MrBayes) to new hampshire✨
• bp_nrdb(1)a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases✨
• bp_oligo_count(1)oligo count and frequency✨
• bp_process_gadfly(1)Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser✨
• bp_process_sgd(1)Massage SGD annotation flat files into a version suitable for the Generic Genome Browser✨
• bp_revtrans-motif(1)Reverse translate a Profam-like protein motif✨
• bp_search2alnblocks(1)Turn SearchIO parseable reports(s) into a set of aligned blocks✨
• bp_search2gff(1)turn a SearchIO report into GFF✨
• bp_search2table(1)turn SearchIO parseable reports into tab delimited format like NCBI's -m 9✨
• bp_search2tribe(1)Turn SearchIO parseable reports(s) into TRIBE matrix✨
• bp_seq_length(1)lists the number of bases and number of sequences in specified sequence database files✨
• bp_seqconvert(1)generic BioPerl sequence format converter✨
• bp_seqcut(1)cut FASTA sequences with a given range✨
• bp_seqpart(1)Takes one or more sequence files and splits them into a number of load balanced files.✨
• bp_seqret(1)bioperl implementation of sequence fetch from local db (like EMBOSS seqret)✨
• bp_seqretsplit(1)split a sequence (or stream) into a single file per sequence✨
• bp_split_seq(1)splits a sequence into equal sized chunks with an optional overlapping range✨
• bp_sreformat(1)convert sequence formats✨
• bp_taxid4species(1)simple script which returns the NCBI Taxonomic id for a requested species✨
• bp_taxonomy2tree(1)Building a taxonomic tree based on the full lineages of a set of species names✨
• bp_translate_seq(1)translates a sequence✨
• bp_tree2pag(1)convert Bio::TreeIO parseable format trees to pagel format✨
• bp_unflatten_seq(1)unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy✨