Sekcja 1p

• acdcheck  -  cdcheck
• ace
• acidrip  -  a Gtk2::Perl wrapper for MPlayer / Mencoder
• ack-grep  -  grep-like text finder
• add_friends  -  Send friend requests to another user’s friends.
• admin  -  create and administer SCCS files (DEVELOPMENT)
• alias  -  define or display aliases
• alien  -  konwertuje lub instaluje obcy pakiet binarny
• altree  -  Analysing phylogeny trees
• altree-add-S  -  Title...
• altree-convert  -  Title...
• applypatch  -  apply ‘makepatch’ generated script to update a source tree
• approve_friends  -  Approve new friends and post a comment to them
• apt-show-versions  -  Lists available package versions with distribution
• apt-src  -  manage debian source package trees
• ar  -  create and maintain library archives
• asa  -  interpret carriage-control characters
• asp-perl  -  Apache::ASP CGI and command line script processor
• astma2xtm.pl  -  an AsTMa to XTM converter
• at  -  execute commands at a later time
• atoms
• ATR_analysis  -  analyse a smart card ATR
• audio_rename  -  rename an audio file via information got via MP3::Tag.
• autodia_java.pl  -  a perl script using the Autodia modules to create UML Class Diagrams or documents. from code or other data sources.
• autodia.pl  -  a perl script using the Autodia modules to create UML Class Diagrams or documents. from code or other data sources.
• AutoSearch  -  utoSearch -- a web-search tracking application
• awk  -  pattern scanning and processing language
• basename  -  return non-directory portion of a pathname
• basepods  -  print out pod paths for the standard perl manpages
• batch  -  schedule commands to be executed in a batch queue
• bc  -  arbitrary-precision arithmetic language
• beancounter  -  Stock portfolio performance monitor tool
• bg  -  run jobs in the background
• blinkenlights
• bp_aacomp  -  amino acid composition of protein sequences
• bp_biblio  -  bioperl client for accessing and querying a bibliographic repository.
• bp_biofetch_genbank_proxy  -  Caching BioFetch-compatible web proxy for GenBank
• bp_bioflat_index  -  index sequence files using Bio::DB::Flat
• bp_biogetseq  -  sequence retrieval using OBDA registry
• bp_bioperl_application_installer
• bp_blast2tree  -  builds a phylogenetic tree based on a sequence search (FastA,BLAST,HMMER)
• bp_bulk_load_gff  -  Bulk-load a Bio::DB::GFF database from GFF files.
• bp_chaos_plot  -  a chaos plot from DNA and RNA sequences
• bp_classify_hits_kingdom
• bp_composite_LD  -  omposite_LD -i filename.prettybase.txt --sortbyld > outfile
• bp_contig_draw  -  earch_overview -- Render a SearchIO parser report into a simple overview graphic
• bp_dbsplit  -  script to split an input set of database(s) into smaller pieces
• bp_download_query_genbank
• bp_embl2picture  -  Render a Genbank/EMBL sequence file graphically as a png image
• bp_extract_feature_seq  -  extract the corresponding sequence for a specified feature type
• bp_fastam9_to_table  -  turn FASTA -m 9 output into NCBI -m 9 tabular output
• bp_fast_load_gff  -  Fast-load a Bio::DB::GFF database from GFF files.
• bp_feature_draw  -  eature_draw.pl -- Render a Bio::Graphics Feature File
• bp_fetch  -  fetches sequences from bioperl indexed databases
• bp_filter_search  -  filters searchio results, outputting a tab delimited summary
• bp_flanks  -  finding flanking sequences for a variant in a sequence position
• bp_frend  -  rend.pl -- Render a Bio::Graphics Feature File on the web
• bp_gccalc  -  GC content of nucleotide sequences
• bp_genbank2gff  -  Load a Bio::DB::GFF database from GENBANK files.
• bp_genbank2gff3  -  p_genbank2gff3.pl -- Genbank->gbrowse-friendly GFF3
• bp_generate_histogram  -  enerate_histogram.pl -- Generate a histogram of Bio::DB::GFF features
• bp_glyphs1-demo  -  First demo of Bio::Graphics glyphs
• bp_glyphs2-demo  -  Second demo of Bio::Graphics glyphs
• bp_heterogeneity_test  -  a test for distinguishing between selection and population expansion.
• bp_hmmer_to_table  -  turn HMMER output into tabular format
• bp_index  -  indexes files for use by bp_fetch.pl
• bp_load_gff  -  Load a Bio::DB::GFF database from GFF files.
• bp_local_taxonomydb_query  -  query a local TaxonomyDB for species or taxonid
• bp_make_mrna_protein  -  Convert an input mRNA/cDNA sequence into protein using translate() -f/--frame Specifies frame [0,1,2] One can also specify: -t/--terminator ...
• bp_mask_by_search  -  mask sequence(s) based on its alignment results
• bp_meta_gff  -  Get/set Bio::DB::GFF meta-data
• bp_mrtrans  -  implement a transformer of alignments from protein to mrna coordinates
• bp_multi_hmmsearch
• bp_mutate  -  randomly mutagenize a single protein or DNA sequence
• bp_nexus2nh  -  convert nexus format trees (from PAUP* and MrBayes) to new hampshire

Książki warte uwagi