Sendu Bala
and 1 contributors

Documentation

  • deob_index.pl - extracts BioPerl documentation and indexes it in a database for easy retrieval
  • authors.pl - check modules and scripts for authors not in AUTHORS file
  • check_NAMEs.pl - check NAME in module POD has fully qualified object name
  • check_URLs.pl - validate URLs located in module code and POD
  • modules.pl - information about modules in BioPerl core
  • pod.pl - check the POD documentation syntax in modules and scripts
  • symlink_script.pl - install script to create symbolic links
  • aacomp - amino acid composition of protein sequences
  • biblio.PLS - bioperl client for accessing and querying a bibliographic repository.
  • biofetch_genbank_proxy.pl - Caching BioFetch-compatible web proxy for GenBank
  • bioflat_index.pl - index sequence files using Bio::DB::Flat
  • biogetseq - sequence retrieval using OBDA registry
  • tree_from_seqsearch - builds a phylogenetic tree based on a sequence search (FastA,BLAST,HMMER)
  • bulk_load_gff.pl - Bulk-load a Bio::DB::GFF database from GFF files.
  • chaos_plot - a chaos plot from DNA and RNA sequences
  • classify_hits_kingdom - classify BLAST hits by taxonomic kingdom
  • composite_LD
  • search_overview - Render a SearchIO parser report into a simple overview graphic
  • dbsplit - script to split an input set of database(s) into smaller pieces
  • bp_embl2picture.pl - Render a Genbank/EMBL sequence file graphically as a png image
  • extract_feature_seq - extract the corresponding sequence for a specified feature type
  • bp_fast_load_gff.pl - Fast-load a Bio::DB::GFF database from GFF files.
  • fastm9_to_table - turn FASTA -m 9 output into NCBI -m 9 tabular output
  • feature_draw.pl - Render a Bio::Graphics Feature File
  • bp_fetch.pl - fetches sequences from bioperl indexed databases
  • filter_search - filters searchio results, outputting a tab delimited summary
  • flanks - finding flanking sequences for a variant in a sequence position
  • frend.pl - Render a Bio::Graphics Feature File on the web
  • gccalc - GC content of nucleotide sequences
  • bp_genbank2gff.pl - Load a Bio::DB::GFF database from GENBANK files.
  • bp_genbank2gff3.pl - Genbank-gtgbrowse-friendly GFF3
  • generate_histogram.pl - Generate a histogram of Bio::DB::GFF features
  • bp_glyphs1-demo.pl - First demo of Bio::Graphics glyphs
  • bp_glyphs2-demo.pl - Second demo of Bio::Graphics glyphs
  • heterogeneity_test - a test for distinguishing between selection and population expansion.
  • hmmer_to_table - turn HMMER output into tabular format
  • bp_index.pl - indexes files for use by bp_fetch.pl
  • bp_load_gff.pl - Load a Bio::DB::GFF database from GFF files.
  • local_taxonomydb_query - query a local TaxonomyDB for species or taxonid
  • make_mrna_protein - Convert an input mRNA/cDNA sequence into protein
  • mask_by_search - mask sequence(s) based on its alignment results
  • bp_meta_gff.pl - Get/set Bio::DB::GFF meta-data
  • bp_mrtrans - implement a transformer of alignments from protein to mrna coordinates
  • mutate.pl - randomly mutagenize a single protein or DNA sequence
  • nexus2nh - convert nexus format trees (from PAUP* and MrBayes) to new hampshire
  • bp_nrdb.PLS - a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases
  • oligo_count - oligo count and frequency
  • pairwise_kaks - script to calculate pairwise Ka,Ks for a set of sequences
  • parse_hmmsearch - parse single/multiple HMMSEARCH results file(s) with different output options
  • process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
  • process_sgd.pl - Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
  • process_wormbase.pl - Massage WormBase GFF files into a version suitable for the Generic Genome Browser
  • query_entrez_taxa - query Entrez taxonomy database and print out information
  • remote_blast.pl - script for submitting jobs to a remote blast server (ncbi blast queue at this time)
  • search2bsml - Turn SearchIO parseable reports(s) into a BSML report
  • search2alnblocks - Turn SearchIO parseable reports(s) into a set of aligned blocks
  • search2gff - Turn SearchIO parseable reports(s) into a GFF report
  • search2table - turn SearchIO parseable reports into tab delimited format like NCBI's -m 9
  • search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix
  • search_overview - Render a SearchIO parser report into a simple overview graphic
  • seq_length.pl - lists the number of bases and number of sequences in specified sequence database files
  • seqconvert - generic BioPerl sequence format converter
  • bp_seqret - bioperl implementation of sequence fetch from local db (like EMBOSS seqret)
  • split_seq - splits a sequence into equal sized chunks with an optional overlapping range
  • bpsreformat - convert sequence formats
  • taxid4species:
  • taxonomy2tree - Building a taxonomic tree based on the full lineages of a set of species names
  • translate_seq - translates a sequence
  • tree2pag - convert Bio::TreeIO parseable format trees to pagel format
  • unflatten_seq - unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy

Modules

Provides

Examples