Section 1 of the manual describes user commands and tools, for example, file manipulation tools, shells, compilers, web browsers, file and image viewers and editors, and so on.
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- bowtie-build
- building a colorspace index for bowtie
- bowtie-debug
- bowtie-align-s - ultrafast memory-efficient short read aligner
- bowtie-inspect-debug
- bowtie-inspect - extracts information from a bowtie index
- bowtie-inspect
- extracts information from a bowtie index
- bowtie
- align-s - ultrafast memory-efficient short read aligner
- bowtie2-align-l
- ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences
- bowtie2-align-s
- ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences
- bowtie2-build-l
- building a colorspace index for bowtie2
- bowtie2-build-s
- building a colorspace index for bowtie2
- bowtie2-build
- wrapper for bowtie2-build-*
- bowtie2-inspect-l
- extracts information from a bowtie2 index
- bowtie2-inspect-s
- extracts information from a bowtie2 index
- bowtie2-inspect
- wrapper for bowtie2-inspect-* index
- bowtie2
- wrapper for bowtie2-align-*
- boxTurb
- part of OpenFOAM (The Open Source CFD Toolbox)
- boxer
- boxer command line utils
- boxes
- text mode box and comment drawing filter
- boxshade
- Pretty-printing of multiple sequence alignments
- bp-analyze
- Generate an HTML report summarizing bali-phy runs
- bp_aacomp
- amino acid composition of protein sequences
- bp_bioflat_index
- bp_bioflat_index.pl - index sequence files using Bio::DB::Flat
- bp_biogetseq
- sequence retrieval using OBDA registry
- bp_dbsplit
- script to split an input set of database(s) into smaller pieces
- bp_extract_feature_seq
- extract the corresponding sequence for a specified feature type
- bp_fastam9_to_table
- fastm9_to_table - turn FASTA -m 9 output into NCBI -m 9 tabular output
- bp_fetch
- bp_fetch.pl - fetches sequences from bioperl indexed databases
- bp_filter_search
- filters searchio results, outputting a tab delimited summary
- bp_find-blast-matches
- bp_find-blast-matches.pl - extract DNA sequences based on BLAST hits
- bp_flanks
- finding flanking sequences for a variant in a sequence position
- bp_gccalc
- GC content of nucleotide sequences
- bp_genbank2gff3
- bp_genbank2gff3.pl -- Genbank->gbrowse-friendly GFF3
- bp_hmmer_to_table.pl
- bp_hmmer_to_table - turn HMMER output into tabular format
- bp_index
- bp_index.pl - indexes files for use by bp_fetch.pl
- bp_local_taxonomydb_query
- query a local TaxonomyDB for species or taxonid
- bp_make_mrna_protein
- Convert an input mRNA/cDNA sequence into protein
- bp_mask_by_search
- mask sequence(s) based on its alignment results
- bp_mrtrans
- implement a transformer of alignments from protein to mrna coordinates
- bp_multi_hmmsearch.pl
- multi_hmmsearch - perform a hmmsearch into multiple FASTA files using an INDEX file
- bp_mutate
- bp_mutate.pl - randomly mutagenize a single protein or DNA sequence
- bp_nexus2nh
- convert nexus format trees (from PAUP* and MrBayes) to new hampshire
- bp_nrdb
- bp_nrdb.PLS - a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases
- bp_oligo_count
- oligo count and frequency
- bp_pairwise_kaks
- calculate pairwise Ka,Ks for a set of sequences
- bp_panalysis.pl
- panalysis.PLS - An example/tutorial script how to access analysis tools
- bp_papplmaker.pl
- papplmaker.PLS - Analysis tools module generator
- bp_parse_hmmsearch.pl
- bp_parse_hmmsearch - parse single/multiple HMMSEARCH results file(s) with different output options
- bp_process_gadfly
- bp_process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
- bp_process_sgd
- bp_process_sgd.pl - Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
- bp_remote_blast.pl
- script for submitting jobs to a remote blast server (ncbi blast queue at this time)
- bp_revtrans-motif
- Reverse translate a Profam-like protein motif
- bp_run_neighbor.pl
- run_neighbor - run Phylip's 'neighbor' program through Bioperl
- bp_run_protdist.pl
- run_neighbor - run Phylip's 'protdist' program through Bioperl
- bp_search2alnblocks
- Turn SearchIO parseable reports(s) into a set of aligned blocks
- bp_search2gff
- turn a SearchIO report into GFF
- bp_search2table
- turn SearchIO parseable reports into tab delimited format like NCBI's -m 9
- bp_search2tribe
- Turn SearchIO parseable reports(s) into TRIBE matrix
- bp_seq_length
- bp_seq_length.pl - lists the number of bases and number of sequences in specified sequence database files
- bp_seqconvert
- generic BioPerl sequence format converter
- bp_seqcut
- bp_seqcut.pl - cut FASTA sequences with a given range
- bp_seqpart
- bp_seqpart.pl - Takes one or more sequence files and splits them into a number of load balanced files
- bp_seqret
- bioperl implementation of sequence fetch from local db (like EMBOSS seqret)
- bp_seqretsplit
- split a sequence (or stream) into a single file per sequence
- bp_split_seq
- splits a sequence into equal sized chunks with an optional overlapping range
- bp_sreformat
- bpsreformat - convert sequence formats
- bp_taxid4species
- simple script which returns the NCBI Taxonomic id for a requested species
- bp_taxonomy2tree
- Building a taxonomic tree based on the full lineages of a set of species names
- bp_translate_seq
- translates a sequence
- bp_tree2pag
- convert Bio::TreeIO parseable format trees to pagel format
- bp_unflatten_seq
- unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy
- bpf-addr2line
- addr2line - convert addresses or symbol+offset into file names and line numbers
- bpf-ar
- ar - create, modify, and extract from archives
- bpf-as
- AS - the portable GNU assembler
- bpf-c++filt
- c++filt - demangle C++ and Java symbols
- bpf-dlltool
- dlltool - create files needed to build and use DLLs
- bpf-elfedit
- elfedit - update ELF header and program property of ELF files
- bpf-gprof
- gprof - display call graph profile data
- bpf-ld
- ld - The GNU linker
- bpf-ld.bfd
- ld - The GNU linker
- bpf-nm
- nm - list symbols from object files
- bpf-objcopy
- objcopy - copy and translate object files
- bpf-objdump
- objdump - display information from object files
- bpf-ranlib
- ranlib - generate an index to an archive
- bpf-readelf
- readelf - display information about ELF files
- bpf-size
- size - list section sizes and total size of binary files
- bpf-strings
- strings - print the sequences of printable characters in files
- bpf-strip
- strip - discard symbols and other data from object files
- bpf-windmc
- windmc - generates Windows message resources
- bpf-windres
- windres - manipulate Windows resources
- bplay
- bplay, brec - buffered sound recording/playing
- bpm-graph
- bpm-tools - calculate the tempo of music files
- bpm-tag
- bpm-tools - calculate the tempo of music files
- bpm
- tools - calculate the tempo of music files
- bppalnoptim
- Sequence alignment optimization according to the number of sequences vs. number of sites trade-off
- bppalnscore
- Bio++ alignment scoring
- bppancestor
- bppml - Ancestral sequence reconstruction with Bio++
- bppconsense
- Tree consensus analysis with Bio++
- bppdist
- Distance methods for phylogenetic reconstruction with Bio++
- bppmixedlikelihoods
- Computation of site per site likelihoods of components of mixture models.
- bppml
- Maximum likelihood phylogenetic analysis with Bio++
- bpppars
- Parsimony phylogenetic analysis with Bio++