section 1 · User commands 💻

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F (continued)

famap(1)prepare Fasta sequence database for re-PCR searches✨
famdef(1)repeatmaker helper to define families✨
fangfrisch(1)update and verify unofficial Clam Anti-Virus signatures✨
fantasdic(1)Versatile dictionary application✨
fapg(1)Fast Audio Playlist Generator✨
faqpods(1)print out pod paths for the standard perl faqs✨
faqpods(1p)print out pod paths for the standard perl faqs✨
far2l(1)Two-panel file manager, with built-in terminal and other usefulness´es.✨
far2ledit(1)Two-panel file manager, with built-in terminal and other usefulness´es.✨
farcompilestrings(1)store compiled FSTs in a finite-state archive✨
farconvert(1)manual page for farconvert 1.8.4✨
farcreate(1)create a finite-state archive from input FSTs✨
farencode(1)manual page for farencode 1.8.4✨
farequal(1)test if two finite-state archives have equal contents✨
farextract(1)extract FSTs from a finite-state archive✨
farinfo(1)query a finite-state archive✨
farisomorphic(1)test if the FSTs in two finite-state archives are isomorphic✨
farm-run.pl(1)helps running maq jobs in batch mode✨
farprintstrings(1)print FSTs in a finite-state archive as strings✨
fasd(1)quick access to files and directories✨
fasm(1)fast assembler for the x86 and x86-64 architectures✨
fast-discovery-server(1)centralized broker for DDS service discovery✨
fast4-g(1)convert a FASTGEN4 file to a BRL-CAD geometry database✨
Fast5_to_seq_summary(1)generate a sequencing summary like file from a directory containing Fast5 files✨
fasta-nr(1)Keep the first of identical sequences✨
fasta2DAM(1)manage nucleotide sequencing read data for the Dazzler assembler✨
fasta2DB(1)manage nucleotide sequencing read data for the Dazzler assembler✨
fasta2esd(1)suite for investigating DNA and RNA sequence similarities✨
fasta2gsi(1)detection of transfer RNA genes in genomic sequence✨
fasta36(1)scan a protein or DNA sequence library for similar sequences fastx36 - compare a DNA sequence to a protein sequence database, comparing the translated DNA sequence in forward and reverse frames…✨
fasta_to_raw(1)Convert fasta to raw input for pscan_chip✨
fastaannotatecdna(1)suite for investigating DNA and RNA sequence similarities✨
fastachecksum(1)suite for investigating DNA and RNA sequence similarities✨
fastaclean(1)suite for investigating DNA and RNA sequence similarities✨
fastaclip(1)suite for investigating DNA and RNA sequence similarities✨
fastacomposition(1)suite for investigating DNA and RNA sequence similarities✨
fastadiff(1)suite for investigating DNA and RNA sequence similarities✨
fastaexplod(1)split multi sequence FastA file into one file per sequence✨
fastaexplode(1)suite for investigating DNA and RNA sequence similarities✨
fastafetch(1)suite for investigating DNA and RNA sequence similarities✨
fastahack(1)fastahack - indexing and extracting sequences and subsequences from FASTA files✨
fastahardmask(1)suite for investigating DNA and RNA sequence similarities✨
fastaindex(1)suite for investigating DNA and RNA sequence similarities✨
fastalength(1)suite for investigating DNA and RNA sequence similarities✨
fastANI(1)Fast alignment-free computation of whole-genome Average Nucleotide Identity✨
fastanrdb(1)suite for investigating DNA and RNA sequence similarities✨
fastaoverlap(1)suite for investigating DNA and RNA sequence similarities✨
fastapi(1)FastAPI CLI – The fastapi command line app. 😎✨
fastapi-cloud(1)Manage FastAPI Cloud deployments.✨
fastapi-cloud-apps(1)Manage your FastAPI Cloud apps.✨
fastapi-cloud-apps-create(1)Create a FastAPI Cloud app.✨
fastapi-cloud-apps-get(1)Get a FastAPI Cloud app by ID.✨
fastapi-cloud-apps-link(1)Link a local directory to an existing FastAPI Cloud app.✨
fastapi-cloud-apps-list(1)List FastAPI Cloud apps.✨
fastapi-cloud-apps-logs(1)Stream or fetch logs from your deployed app.✨
fastapi-cloud-apps-unlink(1)Unlink by deleting the .fastapicloud/cloud.json file.✨
fastapi-cloud-apps-update(1)Update FastAPI Cloud app metadata.✨
fastapi-cloud-auth(1)Authenticate with FastAPI Cloud.✨
fastapi-cloud-auth-login(1)Login to FastAPI Cloud.✨
fastapi-cloud-auth-wait(1)Wait for a device authorization flow to complete.✨
fastapi-cloud-ci(1)Manage CI integration helpers.✨
fastapi-cloud-ci-print-workflow(1)Prints the GitHub Actions workflow YAML without writing files or secrets.✨
fastapi-cloud-ci-setup(1)Configures a GitHub Actions workflow for deploying the app on push to the specified branch.✨
fastapi-cloud-deploy(1)Deploy a FastAPI app to FastAPI Cloud. 🚀✨
fastapi-cloud-deployments(1)Manage the deployments of your app.✨
fastapi-cloud-deployments-build-logs(1)Stream or fetch build logs for a FastAPI Cloud deployment.✨
fastapi-cloud-deployments-get(1)Get a FastAPI Cloud deployment by ID.✨
fastapi-cloud-deployments-list(1)List FastAPI Cloud deployments for an app.✨
fastapi-cloud-env(1)Manage the environment variables of your app.✨
fastapi-cloud-env-delete(1)Delete an environment variable from the app.✨
fastapi-cloud-env-get(1)Get an environment variable for the app.✨
fastapi-cloud-env-list(1)List the environment variables for the app.✨
fastapi-cloud-env-set(1)Set an environment variable for the app.✨
fastapi-cloud-integrations(1)Manage third-party integrations.✨
fastapi-cloud-integrations-providers(1)Manage integration providers for a team.✨
fastapi-cloud-integrations-providers-list(1)List integration providers and their connection status for a team.✨
fastapi-cloud-integrations-resources(1)Manage resources connected to an app.✨
fastapi-cloud-integrations-resources-connect(1)Open FastAPI Cloud to connect a provider resource to an app.✨
fastapi-cloud-integrations-resources-disconnect(1)List resources connected to an app.✨
fastapi-cloud-integrations-resources-get(1)Get a resource connected to an app.✨
fastapi-cloud-integrations-resources-list(1)List resources connected to an app.✨
fastapi-cloud-link(1)Link a local directory to an existing FastAPI Cloud app.✨
fastapi-cloud-login(1)Login to FastAPI Cloud.✨
fastapi-cloud-logout(1)Logout from FastAPI Cloud.✨
fastapi-cloud-logs(1)Stream or fetch logs from your deployed app.✨
fastapi-cloud-setup-ci(1)Configures a GitHub Actions workflow for deploying the app on push to the specified branch.✨
fastapi-cloud-teams(1)Manage your FastAPI Cloud teams.✨
fastapi-cloud-teams-get(1)Get a FastAPI Cloud team by ID.✨
fastapi-cloud-teams-list(1)List FastAPI Cloud teams.✨
fastapi-cloud-tokens(1)Manage deploy tokens for your app.✨
fastapi-cloud-tokens-create(1)Create a deploy token for an app.✨
fastapi-cloud-tokens-delete(1)Delete a deploy token for an app.✨
fastapi-cloud-tokens-list(1)List deploy tokens for an app.✨
fastapi-cloud-unlink(1)Unlink by deleting the .fastapicloud/cloud.json file.✨
fastapi-cloud-whoami(1)Show the currently logged in user.✨
fastapi-deploy(1)Deploy a FastAPI app to FastAPI Cloud. 🚀✨
fastapi-dev(1)Run a FastAPI app in development mode. 🧪✨
fastapi-login(1)Login to FastAPI Cloud. 🚀✨
fastapi-logout(1)Logout from FastAPI Cloud. 🚀✨
fastapi-new(1)Create a new FastAPI project in one command✨
fastapi-run(1)Run a FastAPI app in production mode. 🚀✨
fastaq(1)FASTA and FASTQ file manipulation tools✨
fastaq-acgtn_only(1)Replace every non acgtnACGTN with an N✨
fastaq-add_indels(1)Deletes or inserts bases at given position(s)✨
fastaq-caf_to_fastq(1)Converts a CAF file to FASTQ format✨
fastaq-capillary_to_pairs(1)Converts file of capillary reads to paired and unpaired files✨
fastaq-chunker(1)Splits sequences into equal sized chunks✨
fastaq-count_sequences(1)Counts the sequences in input file✨
fastaq-deinterleave(1)Splits interleaved paired file into two separate files✨
fastaq-enumerate_names(1)Renames sequences in a file, calling them 1,2,3... etc✨
fastaq-expand_nucleotides(1)Makes every combination of degenerate nucleotides✨
fastaq-fasta_to_fastq(1)Convert FASTA and .qual to FASTQ✨
fastaq-filter(1)Filter sequences to get a subset of them✨
fastaq-get_ids(1)Get the ID of each sequence✨
fastaq-get_seq_flanking_gaps(1)Gets the sequences flanking gaps✨
fastaq-interleave(1)Interleaves two files, output is alternating between fwd/rev reads✨
fastaq-make_random_contigs(1)Make contigs of random sequence✨
fastaq-merge(1)Converts multi sequence file to a single sequence✨
fastaq-replace_bases(1)Replaces all occurrences of one letter with another✨
fastaq-reverse_complement(1)Reverse complement all sequences✨
fastaq-scaffolds_to_contigs(1)Creates a file of contigs from a file of scaffolds✨
fastaq-search_for_seq(1)Find all exact matches to a string (and its reverse complement)✨
fastaq-sequence_trim(1)Trim exact matches to a given string off the start of every sequence✨
fastaq-sort_by_name(1)Sorts sequences in lexographical (name) order✨
fastaq-sort_by_size(1)Sorts sequences in length order✨
fastaq-split_by_base_count(1)Split multi sequence file into separate files✨
fastaq-strip_illumina_suffix(1)Strips /1 or /2 off the end of every read name✨
fastaq-to_boulderio(1)Converts to Boulder-IO format, used by primer3✨
fastaq-to_fake_qual(1)Make fake quality scores file✨
fastaq-to_fasta(1)Converts a variety of input formats to nicely formatted FASTA format✨
fastaq-to_mira_xml(1)Create an xml file from a file of reads, for use with Mira assembler✨
fastaq-to_orfs_gff(1)Writes a GFF file of open reading frames✨
fastaq-to_perfect_reads(1)Make perfect paired reads from reference✨
fastaq-to_random_subset(1)Make a random sample of sequences (and optionally mates as well)✨
fastaq-to_tiling_bam(1)Make a BAM file of reads uniformly spread across the input reference✨
fastaq-to_unique_by_id(1)Remove duplicate sequences, based on their names. Keep longest seqs✨
fastaq-translate(1)Translate all sequences in input nucleotide sequences✨
fastaq-trim_contigs(1)Trims a set number of bases off the end of every contig✨
fastaq-trim_ends(1)Trim fixed number of bases of start and/or end of every sequence✨
fastaq-trim_Ns_at_end(1)Trims all Ns at the start/end of all sequences✨
fastaq-version(1)Print version number and exit✨
fastareformat(1)suite for investigating DNA and RNA sequence similarities✨
fastaremove(1)suite for investigating DNA and RNA sequence similarities✨
fastarevcomp(1)suite for investigating DNA and RNA sequence similarities✨
fastaseqs(1)converts a file of sequences to FASTA format✨
fastasoftmask(1)suite for investigating DNA and RNA sequence similarities✨
fastasort(1)suite for investigating DNA and RNA sequence similarities✨
fastasplit(1)suite for investigating DNA and RNA sequence similarities✨
fastasubseq(1)suite for investigating DNA and RNA sequence similarities✨
fastatranslate(1)suite for investigating DNA and RNA sequence similarities✨
FastaUnique(1)remove noise from high throughput nucleotide sequence data✨
fastautils(1)FASTA format file manipulation utilities✨
fastavalidcds(1)suite for investigating DNA and RNA sequence similarities✨
fastavro(1)fastavro Documentation The current Python avro package is dog slow. On a test case of about 10K records, it takes about 14sec to iterate over all of them. In comparison the JAVA avro SDK does it in…✨
fastbase64(1)base64 encode/decode data and print to standard output✨
fastbase64.coreutils(1)base64 encode/decode data and print to standard output (coreutils compatible)✨
fastBlockSearch(1)search loci matching protein block profiles✨
fastboot(1)Android flashing and booting utility✨
fastcgi-mono-server(1)Mono ASP.NET Web Server (xsp and xsp2)✨
fastcgi-mono-server4(1)Mono ASP.NET Web Server (xsp and xsp2)✨
fastchess(1)a command-line tool for managing chess games with engines✨
fastconv-float(1)Direct Fast Fourier Transformation CLI tool✨
fastconvr-float(1)Reverse Fast Fourier Transformation CLI tool✨
fastd(1)Fast and Secure Tunnelling Daemon✨
fastdds(1)FastDDS tool✨
fastddsgen(1)IDL source code generator✨
fastDNAml(1)DNA Maximum Likelihood program✨
fastDNAml-util(1)DNA Maximum Likelihood program✨
fastep(1)Adjust python project to use fastentrypoints✨
fastf3(1)compare a mixed peptide sequence against a protein database using a modified fasta algorithm. tfastf3, tfastf3_t - compare a mixed pepide sequence against a translated DNA database.✨
fastfetch(1)A fast and feature-rich system information tool similar to neofetch✨
fastforward(1)forward mail according to a cdb database✨
fastjar(1)archive tool for Java archives✨
fastjet-config(1)fastjet-config✨
fastml(1)maximum likelihood ancestral amino-acid sequence reconstruction✨
fastnetmon_client(1)show information about top talkers and detected DDoS attacks✨
fastp(1)Ultra-fast all-in-one FASTQ preprocessor✨
fastq-clipper(1)ea-utils: removes one or more adapter sequences from the fastq file✨
fastq-interleave(1)Read 2 fastq files, and write them interleaved✨
fastq-join(1)ea-utils: join two paired-end reads on the overlapping ends✨
fastq-mcf(1)ea-utils: detect levels of adapter presence, compute likelihoods and locations of the adapters✨
fastq-multx(1)ea-utils: replace % with the barcode id in the barcodes file✨
fastq-stats(1)ea-utils: produce lots of easily digested statistics✨
fastq_pair(1)Rewrite paired end fastq files so that all reads have a mate and to separate out singletons✨
fastqc(1)high throughput sequence QC analysis tool SYNOPSIS fastqc seqfile1 seqfile2 .. seqfileN fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam] [-c contaminant file] seqfile1 .. seqfileN✨
fastQTL(1)Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes✨
fastqtobam(1)convert FastQ to unmapped BAM✨
fastrm(1)Quickly remove a list of files✨
fastrtpsgen(1)IDL source code generator✨
fasts3(1)compare several short peptide sequences against a protein database using a modified fasta algorithm. tfasts3, tfasts3_t - compare short pepides against a translated DNA database.✨
fasttext(1)Library for efficient learning of word representations and sentence classification✨
fasttracker2(1)Fasttracker II clone to track music✨
FastTree(1)create phylogenetic trees from alignments of nucleotide or protein sequences✨
fasttree(1)create phylogenetic trees from alignments of nucleotide or protein sequences✨
fasttreeMP(1)create phylogenetic trees from alignments of nucleotide or protein sequences (openMP version)✨
fastx-graph(1)ea-utils: R script to process fastq-stats output✨
fatattr(1)Display or change attributes on a FAT filesystem✨
fatcat(1)FAT filesystem explore, extract, repair, and forensic tool✨
fathom(1)sequence and annotation tool✨
fatou(1)Fatou: a language server, formatter, and linter for Julia✨