[ 原始碼： debian-med ]
套件：med-bio（3.8.1）
Debian Med bioinformatics packages
This metapackage will install Debian packages for use in molecular biology, structural biology and other biological sciences.
其他與 med-bio 有關的套件
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- dep: med-config (= 3.8.1)
- Debian Med general config package
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- dep: med-tasks (= 3.8.1)
- Debian Med tasks for tasksel
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- rec: abacas
- close gaps in genomic alignments from short reads
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- rec: abpoa
- adaptive banded Partial Order Alignment
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- rec: abyss
- de novo, parallel, sequence assembler for short reads
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- rec: acedb-other
- retrieval of DNA or protein sequences
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- rec: adapterremoval
- rapid adapter trimming, identification, and read merging of gene sequences
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- rec: adun-core
- Molecular Simulator
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- rec: aegean
- integrated genome analysis toolkit
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- rec: aevol
- digital genetics model to run Evolution Experiments in silico
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- rec: alien-hunter
- Interpolated Variable Order Motifs to identify horizontally acquired DNA
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- rec: alter-sequence-alignment
- genomic sequences ALignment Transformation EnviRonment
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- rec: altree
- program to perform phylogeny-based association and localization analysis
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- rec: amap-align
- Protein multiple alignment by sequence annealing
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- rec: ampliconnoise
- removal of noise from 454 sequenced PCR amplicons
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- rec: andi
- Efficient Estimation of Evolutionary Distances
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- rec: any2fasta
- convert various sequence formats to FASTA
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- rec: aragorn
- tRNA and tmRNA detection in nucleotide sequences
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- rec: arden
- specificity control for read alignments using an artificial reference
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- rec: ariba
- Antibiotic Resistance Identification By Assembly
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- rec: art-nextgen-simulation-tools
- simulation tools to generate synthetic next-generation sequencing reads
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- rec: artemis
- genome browser and annotation tool
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- rec: artfastqgenerator
- outputs artificial FASTQ files derived from a reference genome
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- rec: assembly-stats
- get assembly statistics from FASTA and FASTQ files
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- rec: assemblytics
- detect and analyze structural variants from a genome assembly
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- rec: atac
- genome assembly-to-assembly comparison
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- rec: ataqv
- ATAC-seq QC and visualization
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- rec: atropos
- NGS read trimming tool that is specific, sensitive, and speedy
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- rec: augur
- pipeline components for real-time virus analysis
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- rec: augustus
- gene prediction in eukaryotic genomes
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- rec: autodock
- analysis of ligand binding to protein structure
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- rec: autodock-vina
- docking of small molecules to proteins
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- rec: autogrid
- pre-calculate binding of ligands to their receptor
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- rec: avogadro
- Molecular Graphics and Modelling System
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- rec: axe-demultiplexer
- Trie-based DNA sequencing read demultiplexer
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- rec: baitfisher
- software package for designing hybrid enrichment probes
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- rec: bali-phy
- Bayesian Inference of Alignment and Phylogeny
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- rec: ballview
- free molecular modeling and molecular graphics tool
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- rec: bamclipper
- Remove gene-specific primer sequences from SAM/BAM alignments
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- rec: bamkit
- tools for common BAM file manipulations
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- rec: bamtools
- toolkit for manipulating BAM (genome alignment) files
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- rec: bandage
- Bioinformatics Application for Navigating De novo Assembly Graphs Easily
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- rec: barrnap
- rapid ribosomal RNA prediction
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- rec: bbmap
- BBTools genomic aligner and other tools for short sequences
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- rec: bcalm
- de Bruijn compaction in low memory
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- rec: bcftools
- genomic variant calling and manipulation of VCF/BCF files
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- rec: beads
- 2-DE electrophoresis gel image spot detection
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- rec: beagle
- Genotype calling, genotype phasing and imputation of ungenotyped markers
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- rec: beast-mcmc
- Bayesian MCMC phylogenetic inference
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- rec: beast2-mcmc
- Bayesian MCMC phylogenetic inference
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- rec: bedops
- high-performance genomic feature operations
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- rec: bedtools
- suite of utilities for comparing genomic features
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- rec: belvu
- multiple sequence alignment viewer and phylogenetic tool
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- rec: berkeley-express
- Streaming quantification for high-throughput sequencing
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- rec: bio-eagle
- Haplotype phasing within a genotyped cohort or using a phased reference panel
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- rec: bio-rainbow
- clustering and assembling short reads for bioinformatics
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- rec: bio-tradis
- analyse the output from TraDIS analyses of genomic sequences
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- rec: bio-vcf
- domain specific language (DSL) for processing the VCF format
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- rec: bioawk
- extension of awk for biological sequence analysis
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- rec: biobambam2
- tools for early stage alignment file processing
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- rec: biosyntax
- Syntax Highlighting for Computational Biology (metapackage)
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- rec: bitseq
- Bayesian Inference of Transcripts from Sequencing Data
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- rec: blasr
- mapping single-molecule sequencing reads
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- rec: blixem
- interactive browser of sequence alignments
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- rec: bolt-lmm
- Efficient large cohorts genome-wide Bayesian mixed-model association testing
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- rec: bowtie
- Ultrafast memory-efficient short read aligner
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- rec: bowtie2
- ultrafast memory-efficient short read aligner
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- rec: boxshade
- Pretty-printing of multiple sequence alignments
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- rec: bppphyview
- Bio++ Phylogenetic Viewer
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- rec: bppsuite
- Bio++ program suite
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- rec: brig
- BLAST Ring Image Generator
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- rec: btllib-tools
- Bioinformatics Technology Lab common code library tools
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- rec: busco
- benchmarking sets of universal single-copy orthologs
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- rec: bustools
- program for manipulating BUS files for single cell RNA-Seq datasets
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- rec: bwa
- Burrows-Wheeler Aligner
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- rec: canu
- single molecule sequence assembler for genomes
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- rec: cassiopee
- index and search tool in genomic sequences
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- rec: cat-bat
- taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
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- rec: cct
- visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
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- rec: cd-hit
- suite of programs designed to quickly group sequences
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- rec: cdbfasta
- Constant DataBase indexing and retrieval tools for multi-FASTA files
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- rec: centrifuge
- rapid and memory-efficient system for classification of DNA sequences
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- rec: cgview
- Circular Genome Viewer
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- rec: changeo
- Repertoire clonal assignment toolkit (Python 3)
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- rec: chimeraslayer
- detects likely chimeras in PCR amplified DNA
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- rec: chromhmm
- Chromatin state discovery and characterization
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- rec: chromimpute
- Large-scale systematic epigenome imputation
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- rec: cif-tools
- Suite of tools to manipulate, validate and query mmCIF files
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- rec: circlator
- circularize genome assemblies
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- rec: circos
- plotter for visualizing data
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- rec: clearcut
- extremely efficient phylogenetic tree reconstruction
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- rec: clonalframe
- inference of bacterial microevolution using multilocus sequence data
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- rec: clonalframeml
- Efficient Inference of Recombination in Whole Bacterial Genomes
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- rec: clonalorigin
- inference of homologous recombination in bacteria using whole genome sequences
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- rec: clustalo
- General-purpose multiple sequence alignment program for proteins
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- rec: clustalw
- global multiple nucleotide or peptide sequence alignment
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- rec: clustalx
- Multiple alignment of nucleic acid and protein sequences (graphical interface)
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- rec: cnvkit
- Copy number variant detection from targeted DNA sequencing
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- rec: codonw
- Correspondence Analysis of Codon Usage
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- rec: comet-ms
- Tandem mass spectrometry (MS/MS) search engine
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- rec: concavity
- predictor of protein ligand binding sites from structure and conservation
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- rec: conservation-code
- protein sequence conservation scoring tool
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- rec: covtobed
- convert the coverage track from a BAM file into a BED file
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- rec: crac
- integrated RNA-Seq read analysis
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- rec: csb
- Computational Structural Biology Toolbox (CSB)
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- rec: cutadapt
- Clean biological sequences from high-throughput sequencing reads
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- rec: cutesv
- comprehensive discovery of structural variations of genomic sequences
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- rec: daligner
- local alignment discovery between long nucleotide sequencing reads
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- rec: damapper
- long read to reference genome mapping tool
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- rec: datamash
- statistics tool for command-line interface
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- rec: dawg
- simulate the evolution of recombinant DNA sequences
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- rec: dazzdb
- manage nucleotide sequencing read data
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- rec: delly
- Structural variant discovery by read analysis
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- rec: density-fitness
- Calculates per-residue electron density scores
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- rec: dextractor
- (d)extractor and compression command library
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- rec: dialign
- Segment-based multiple sequence alignment
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- rec: dialign-tx
- Segment-based multiple sequence alignment
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- rec: diamond-aligner
- accelerated BLAST compatible local sequence aligner
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- rec: discosnp
- discovering Single Nucleotide Polymorphism from raw set(s) of reads
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- rec: disulfinder
- cysteines disulfide bonding state and connectivity predictor
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- rec: dnaclust
- tool for clustering millions of short DNA sequences
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- rec: dnarrange
- Method to find rearrangements in long DNA reads relative to a genome seq
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- rec: dotter
- detailed comparison of two genomic sequences
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- rec: drop-seq-tools
- analyzing Drop-seq data
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- rec: dssp
- protein secondary structure assignment based on 3D structure
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- rec: dwgsim
- short sequencing read simulator
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- rec: e-mem
- Efficient computation of Maximal Exact Matches for very large genomes
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- rec: ea-utils
- command-line tools for processing biological sequencing data
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- rec: ecopcr
- estimate PCR barcode primers quality
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- rec: edtsurf
- triangulated mesh surfaces for protein structures
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- rec: eigensoft
- reduction of population bias for genetic analyses
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- rec: elph
- DNA/protein sequence motif finder
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- rec: embassy-domainatrix
- Extra EMBOSS commands to handle domain classification file
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- rec: embassy-domalign
- Extra EMBOSS commands for protein domain alignment
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- rec: embassy-domsearch
- Extra EMBOSS commands to search for protein domains
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- rec: emboss
- European molecular biology open software suite
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- rec: emmax
- genetic mapping considering population structure
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- rec: estscan
- ORF-independent detector of coding DNA sequences
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- rec: examl
- Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
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- rec: exonerate
- generic tool for pairwise sequence comparison
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- rec: fasta3
- tools for searching collections of biological sequences
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- rec: fastahack
- utility for indexing and sequence extraction from FASTA files
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- rec: fastani
- Fast alignment-free computation of whole-genome Average Nucleotide Identity
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- rec: fastaq
- FASTA and FASTQ file manipulation tools
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- rec: fastdnaml
- Tool for construction of phylogenetic trees of DNA sequences
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- rec: fastlink
- faster version of pedigree programs of Linkage
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- rec: fastml
- maximum likelihood ancestral amino-acid sequence reconstruction
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- rec: fastp
- Ultra-fast all-in-one FASTQ preprocessor
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- rec: fastq-pair
- Rewrites paired end fastq so all reads have a mate to separate out singletons
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- rec: fastqc
- quality control for high throughput sequence data
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- rec: fastqtl
- Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes
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- rec: fasttree
- phylogenetic trees from alignments of nucleotide or protein sequences
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- rec: ffindex
- simple index/database for huge amounts of small files
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- rec: figtree
- graphical phylogenetic tree viewer
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- rec: filtlong
- quality filtering tool for long reads of genome sequences
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- rec: fitgcp
- fitting genome coverage distributions with mixture models
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- rec: flash
- Fast Length Adjustment of SHort reads
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- rec: flexbar
- flexible barcode and adapter removal for sequencing platforms
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- rec: flye
- de novo assembler for single molecule sequencing reads using repeat graphs
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- rec: fml-asm
- tool for assembling Illumina short reads in small regions
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- rec: freebayes
- Bayesian haplotype-based polymorphism discovery and genotyping
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- rec: freecontact
- fast protein contact predictor
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- rec: fsa
- Fast Statistical Alignment of protein, RNA or DNA sequences
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- rec: fsm-lite
- frequency-based string mining (lite)
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- rec: gamgi
- General Atomistic Modelling Graphic Interface (GAMGI)
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- rec: garli
- phylogenetic analysis of molecular sequence data using maximum-likelihood
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- rec: garlic
- visualization program for biomolecules
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- rec: gasic
- genome abundance similarity correction
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- rec: gatb-core
- Genome Analysis Toolbox with de-Bruijn graph
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- rec: gbrowse
- GMOD Generic Genome Browser
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- rec: gdpc
- visualiser of molecular dynamic simulations
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- rec: gemma
- Genome-wide Efficient Mixed Model Association
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- rec: genometester
- toolkit for performing set operations on k-mer lists
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- rec: genomethreader
- software tool to compute gene structure predictions
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- rec: genometools
- versatile genome analysis toolkit
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- rec: genomicsdb-tools
- sparse array storage library for genomics (tools)
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- rec: gentle
- suite for molecular cloning and sequence analysis
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- rec: gff2aplot
- pair-wise alignment-plots for genomic sequences in PostScript
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- rec: gff2ps
- produces PostScript graphical output from GFF-files
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- rec: gffread
- GFF/GTF format conversions, region filtering, FASTA sequence extraction
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- rec: ggd-utils
- programs for use in ggd
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- rec: ghemical
- GNOME molecular modelling environment
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- rec: ghmm
- General Hidden-Markov-Model library - tools
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- rec: glam2
- gapped protein motifs from unaligned sequences
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- rec: gmap
- spliced and SNP-tolerant alignment for mRNA and short reads
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- rec: grabix
- wee tool for random access into BGZF files
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- rec: graphlan
- circular representations of taxonomic and phylogenetic trees
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- rec: grinder
- Versatile omics shotgun and amplicon sequencing read simulator
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- rec: gromacs
- Molecular dynamics simulator, with building and analysis tools
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- rec: gsort
- sort genomic data
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- rec: gubbins
- phylogenetic analysis of genome sequences
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- rec: gwama
- Genome-Wide Association Meta Analysis
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- rec: harvest-tools
- archiving and postprocessing for reference-compressed genomic multi-alignments
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- rec: hhsuite
- sensitive protein sequence searching based on HMM-HMM alignment
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- rec: hilive
- realtime alignment of Illumina reads
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- rec: hinge
- long read genome assembler based on hinging
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- rec: hisat2
- graph-based alignment of short nucleotide reads to many genomes
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- rec: hmmer
- profile hidden Markov models for protein sequence analysis
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- rec: hmmer2
- profile hidden Markov models for protein sequence analysis
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- rec: idba
- iterative De Bruijn Graph short read assemblers
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- rec: igblast
- Immunoglobulin and T cell receptor variable domain sequence analysis
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- rec: igor
- infers V(D)J recombination processes from sequencing data
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- rec: igv
- Integrative Genomics Viewer
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- rec: indelible
- powerful and flexible simulator of biological evolution
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- rec: infernal
- inference of RNA secondary structural alignments
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- rec: insilicoseq
- sequencing simulator producing realistic Illumina reads
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- rec: ipig
- integrating PSMs into genome browser visualisations
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- rec: iqtree
- efficient phylogenetic software by maximum likelihood
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- rec: iva
- iterative virus sequence assembler
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- rec: jaligner
- Smith-Waterman algorithm with Gotoh's improvement
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- rec: jalview
- multiple alignment editor
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- rec: jellyfish
- count k-mers in DNA sequences
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- rec: jellyfish1
- count k-mers in DNA sequences
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- rec: jmodeltest
- HPC selection of models of nucleotide substitution
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- rec: jmol
- Molecular Viewer
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- rec: kalign
- Global and progressive multiple sequence alignment
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- rec: kallisto
- near-optimal RNA-Seq quantification
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- rec: kaptive
- obtain information about K and O types for Klebsiella genome assemblies
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- rec: khmer
- in-memory DNA sequence kmer counting, filtering & graph traversal
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- rec: kineticstools
- detection of DNA modifications
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- rec: king-probe
- Evaluate and visualize protein interatomic packing
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- rec: kissplice
- Detection of various kinds of polymorphisms in RNA-seq data
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- rec: kleborate
- tool to screen Klebsiella genome assemblies
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- rec: kma
- mapping genomic sequences to raw reads directly against redundant databases
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- rec: kmc
- count kmers in genomic sequences
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- rec: kmer
- suite of tools for DNA sequence analysis
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- rec: kmerresistance
- correlates mapped genes with the predicted species of WGS samples
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- rec: kraken
- assigning taxonomic labels to short DNA sequences
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- rec: kraken2
- taxonomic classification system using exact k-mer matches
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- rec: lagan
- highly parametrizable pairwise global genome sequence aligner
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- rec: lamarc
- Likelihood Analysis with Metropolis Algorithm using Random Coalescence
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- rec: lamassemble
- Merges overlapping "long" DNA reads into a consensus sequences
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- rec: lambda-align
- Local Aligner for Massive Biological DatA
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- rec: lambda-align2
- Local Aligner for Massive Biological DatA - v2
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- rec: last-align
- genome-scale comparison of biological sequences
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- rec: lastz
- pairwise aligning DNA sequences
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- rec: leaff
- biological sequence library utilities and applications
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- rec: lefse
- determine features of organisms, clades, taxonomic units, genes
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- rec: libpwiz-tools
- ProteoWizard command line tools
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- rec: librg-utils-perl
- parsers and format conversion utilities used by (e.g.) profphd
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- rec: libvcflib-tools
- C++ library for parsing and manipulating VCF files (tools)
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- rec: lighter
- fast and memory-efficient sequencing error corrector
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- rec: logol
- 套件暫時不可用
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- rec: loki
- MCMC linkage analysis on general pedigrees
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- rec: ltrsift
- postprocessing and classification of LTR retrotransposons
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- rec: lucy
- DNA sequence quality and vector trimming tool
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- rec: lumpy-sv
- general probabilistic framework for structural variant discovery
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- rec: macs
- Model-based Analysis of ChIP-Seq on short reads sequencers
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- rec: macsyfinder
- detection of macromolecular systems in protein datasets
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- rec: maffilter
- process genome alignment in the Multiple Alignment Format
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- rec: mafft
- Multiple alignment program for amino acid or nucleotide sequences
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- rec: malt
- sequence alignment and analysis tool to process sequencing data
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- rec: mapdamage
- tracking and quantifying damage patterns in ancient DNA sequences
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- rec: mapsembler2
- bioinformatics targeted assembly software
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- rec: maq
- maps short fixed-length polymorphic DNA sequence reads to reference sequences
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- rec: maqview
- graphical read alignment viewer for short gene sequences
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- rec: mash
- fast genome and metagenome distance estimation using MinHash
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- rec: massxpert
- transitional package for massxpert -> massxpert2
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- rec: mauve-aligner
- multiple genome alignment
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- rec: mcaller
- find methylation in nanopore reads
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- rec: mecat2
- ultra-fast and accurate de novo assembly tools for SMRT reads
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- rec: megadepth
- computes coverage from BigWig and BAM sequencing files
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- rec: megahit
- ultra-fast and memory-efficient meta-genome assembler
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- rec: megan-ce
- interactive tool to explore and analyse microbiome sequencing data
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- rec: melting
- compute the melting temperature of nucleic acid duplex
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- rec: meryl
- in- and out-of-core kmer counting and utilities
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- rec: metabat
- robust statistical framework for reconstructing genomes from metagenomic data
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- rec: metaphlan
- Metagenomic Phylogenetic Analysis
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- rec: metastudent
- predictor of Gene Ontology terms from protein sequence
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- rec: mhap
- locality-sensitive hashing to detect long-read overlaps
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- rec: microbegps
- explorative taxonomic profiling tool for metagenomic data
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- rec: microbiomeutil
- Microbiome Analysis Utilities
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- rec: mindthegap
- performs detection and assembly of DNA insertion variants in NGS read datasets
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- rec: minexpert2
- MS^n mass spectrometric data visualization and mining (runtime)
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- rec: minia
- short-read biological sequence assembler
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- rec: miniasm
- ultrafast de novo assembler for long noisy DNA sequencing reads
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- rec: minimac4
- Fast Imputation Based on State Space Reduction HMM
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- rec: minimap
- tool for approximate mapping of long biosequences such as DNA reads
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- rec: minimap2
- versatile pairwise aligner for genomic and spliced nucleotide sequences
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- rec: mipe
- Tools to store PCR-derived data
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- rec: mira-assembler
- Whole Genome Shotgun and EST Sequence Assembler
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- rec: mirtop
- annotate miRNAs with a standard mirna/isomir naming
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- rec: mlv-smile
- Find statistically significant patterns in sequences
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- rec: mmb
- model the structure and dynamics of macromolecules
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- rec: mmseqs2
- ultra fast and sensitive protein search and clustering
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- rec: mosdepth
- BAM/CRAM depth calculation biological sequencing
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- rec: mothur
- sequence analysis suite for research on microbiota
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- rec: mptp
- single-locus species delimitation
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- rec: mrbayes
- Bayesian Inference of Phylogeny
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- rec: multiqc
- output integration for RNA sequencing across tools and samples
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- rec: mummer
- Efficient sequence alignment of full genomes
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- rec: murasaki
- homology detection tool across multiple large genomes
- 或者 murasaki-mpi
- homology detection tool across multiple large genomes (MPI-version)
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- rec: muscle
- Multiple alignment program of protein sequences
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- rec: muscle3
- multiple alignment program of protein sequences
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- rec: mustang
- multiple structural alignment of proteins
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- rec: nanofilt
- filtering and trimming of long read sequencing data
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- rec: nanolyse
- remove lambda phage reads from a fastq file
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- rec: nanook
- pre- and post-alignment analysis of nanopore sequencing data
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- rec: nanopolish
- consensus caller for nanopore sequencing data
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- rec: nanostat
- statistics on long biological sequences
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- rec: nanosv
- structural variant caller for nanopore data
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- rec: nast-ier
- NAST-based DNA alignment tool
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- rec: ncbi-acc-download
- download genome files from NCBI by accession
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- rec: ncbi-blast+
- next generation suite of BLAST sequence search tools
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- rec: ncbi-blast+-legacy
- NCBI Blast legacy call script
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- rec: ncbi-entrez-direct
- NCBI Entrez utilities on the command line
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- rec: ncbi-epcr
- Tool to test a DNA sequence for the presence of sequence tagged sites
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- rec: ncbi-seg
- tool to mask segments of low compositional complexity in amino acid sequences
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- rec: ncbi-tools-bin
- NCBI libraries for biology applications (text-based utilities)
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- rec: ncbi-tools-x11
- NCBI libraries for biology applications (X-based utilities)
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- rec: ncl-tools
- tools to deal with NEXUS files
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- rec: ncoils
- coiled coil secondary structure prediction
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- rec: neobio
- computes alignments of amino acid and nucleotide sequences
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- rec: ngmlr
- CoNvex Gap-cost alignMents for Long Reads
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- rec: njplot
- phylogenetic tree drawing program
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- rec: norsnet
- tool to identify unstructured loops in proteins
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- rec: norsp
- predictor of non-regular secondary structure
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- rec: ntcard
- Streaming algorithm to estimate cardinality in genomics datasets
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- rec: nxtrim
- Optimized trimming of Illumina mate pair reads
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- rec: obitools
- programs to analyze NGS data in a DNA metabarcoding context
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- rec: openms
- package for LC/MS data management and analysis
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- rec: optimir
- Integrating genetic variations in miRNA alignment
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- rec: pal2nal
- converts proteins to genomic DNA alignment
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- rec: paleomix
- pipelines and tools for the processing of ancient and modern HTS data
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- rec: paml
- Phylogenetic Analysis by Maximum Likelihood (PAML)
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- rec: paraclu
- Parametric clustering of genomic and transcriptomic features
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- rec: parasail
- Aligner based on libparasail
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- rec: parsinsert
- Parsimonious Insertion of unclassified sequences into phylogenetic trees
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- rec: parsnp
- rapid core genome multi-alignment
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- rec: patman
- rapid alignment of short sequences to large databases
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- rec: pbdagcon
- sequence consensus using directed acyclic graphs
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- rec: pbhoney
- genomic structural variation discovery
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- rec: pbjelly
- genome assembly upgrading tool
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- rec: pbsim
- simulator for PacBio sequencing reads
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- rec: pbsuite
- software for Pacific Biosciences sequencing data
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- rec: pdb2pqr
- Preparation of protein structures for electrostatics calculations
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- rec: perlprimer
- Graphical design of primers for PCR
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- rec: perm
- efficient mapping of short reads with periodic spaced seeds
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- rec: pftools
- build and search protein and DNA generalized profiles
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- rec: phast
- phylogenetic analysis with space/time models
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- rec: phipack
- PHI test and other tests of recombination
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- rec: phybin
- binning/clustering newick trees by topology
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- rec: phylip
- package of programs for inferring phylogenies
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- rec: phylonium
- Fast and Accurate Estimation of Evolutionary Distances
-
- rec: phyml
- Phylogenetic estimation using Maximum Likelihood
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- rec: physamp
- sample sequence alignment corresponding to phylogeny
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- rec: phyutility
- simple analyses or modifications on both phylogenetic trees and data matrices
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- rec: phyx
- UNIX-style phylogenetic analyses on trees and sequences
-
- rec: picard-tools
- Command line tools to manipulate SAM and BAM files
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- rec: picopore
- lossless compression of Nanopore files
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- rec: pigx-rnaseq
- pipeline for checkpointed and distributed RNA-seq analyses
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- rec: piler
- genomic repeat analysis
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- rec: pilercr
- software for finding CRISPR repeats
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- rec: pilon
- automated genome assembly improvement and variant detection tool
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- rec: pinfish
- Collection of tools to annotate genomes using long read transcriptomics data
-
- rec: pique
- software pipeline for performing genome wide association studies
-
- rec: pirs
- Profile based Illumina pair-end Reads Simulator
-
- rec: pizzly
- Identifies gene fusions in RNA sequencing data
-
- rec: placnet
- Plasmid Constellation Network project
-
- rec: plasmidid
- mapping-based, assembly-assisted plasmid identification tool
-
- rec: plasmidomics
- draw plasmids and vector maps with PostScript graphics export
-
- rec: plasmidseeker
- identification of known plasmids from whole-genome sequencing reads
-
- rec: plast
- Parallel Local Sequence Alignment Search Tool
-
- rec: plink
- whole-genome association analysis toolset
-
- rec: plink1.9
- whole-genome association analysis toolset
-
- rec: plink2
- whole-genome association analysis toolset
-
- rec: plip
- fully automated protein-ligand interaction profiler
-
- rec: poa
- Partial Order Alignment for multiple sequence alignment
-
- rec: populations
- population genetic software
-
- rec: porechop
- adapter trimmer for Oxford Nanopore reads
-
- rec: poretools
- toolkit for nanopore nucleotide sequencing data
-
- rec: prank
- Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
-
- rec: predictnls
- prediction and analysis of protein nuclear localization signals
-
- rec: presto
- toolkit for processing B and T cell sequences
-
- rec: prime-phylo
- bayesian estimation of gene trees taking the species tree into account
-
- rec: primer3
- tool to design flanking oligo nucleotides for DNA amplification
-
- rec: prinseq-lite
- PReprocessing and INformation of SEQuence data (lite version)
-
- rec: proalign
- Probabilistic multiple alignment program
-
- rec: probabel
- Toolset for Genome-Wide Association Analysis
-
- rec: probalign
- multiple sequence alignment using partition function posterior probabilities
-
- rec: probcons
- PROBabilistic CONSistency-based multiple sequence alignment
-
- rec: proda
- multiple alignment of protein sequences
-
- rec: prodigal
- Microbial (bacterial and archaeal) gene finding program
-
- rec: profbval
- predictor of flexible/rigid protein residues from sequence
-
- rec: profisis
- prediction of protein-protein interaction sites from sequence
-
- rec: profnet-bval
- neural network architecture for profbval
-
- rec: profnet-chop
- neural network architecture for profchop
-
- rec: profnet-con
- neural network architecture for profcon
-
- rec: profnet-isis
- neural network architecture for profisis
-
- rec: profnet-md
- neural network architecture for metadisorder
-
- rec: profnet-norsnet
- neural network architecture for norsnet
-
- rec: profnet-prof
- neural network architecture for profacc
-
- rec: profnet-snapfun
- neural network architecture for snapfun
-
- rec: profphd-net
- neural network architecture for profphd
-
- rec: profphd-utils
- profphd helper utilities convert_seq and filter_hssp
-
- rec: proftmb
- per-residue prediction of bacterial transmembrane beta barrels
-
- rec: progressivemauve
- multiple genome alignment algorithms
-
- rec: prokka
- rapid annotation of prokaryotic genomes
-
- rec: proteinortho
- Detection of (Co-)orthologs in large-scale protein analysis
-
- rec: prottest
- selection of best-fit models of protein evolution
-
- rec: provean
- Protein Variation Effect Analyzer
-
- rec: pscan-chip
- ChIP-based identifcation of TF binding sites
-
- rec: pscan-tfbs
- search for transcription factor binding sites
-
- rec: psortb
- bacterial localization prediction tool
-
- rec: pullseq
- Extract sequence from a fasta or fastq
-
- rec: pycoqc
- computes metrics and generates Interactive QC plots
-
- rec: pycorrfit
- tool for fitting correlation curves on a logarithmic plot
-
- rec: pyensembl
- installs data from the Ensembl genome database
-
- rec: pyfastx
- fast random access to sequences from FASTA/Q file - command
-
- rec: pymol
- Molecular Graphics System
-
- rec: pyscanfcs
- scientific tool for perpendicular line scanning FCS
-
- rec: python3-biomaj3-daemon
- BioMAJ daemon library
-
- rec: python3-cogent3
- framework for genomic biology
-
- rec: python3-emperor
- visualizing high-throughput microbial community data
-
- rec: python3-geneimpacts
- wraps command line tools to assess variants in gene sequences
-
- rec: python3-gffutils
- Work with GFF and GTF files in a flexible database framework
-
- rec: python3-pairtools
- Framework to process sequencing data from a Hi-C experiment
-
- rec: python3-pybedtools
- Python 3 wrapper around BEDTools for bioinformatics work
-
- rec: python3-sqt
- SeQuencing Tools for biological DNA/RNA high-throughput data
-
- rec: python3-treetime
- inference of time stamped phylogenies and ancestral reconstruction (Python 3)
-
- rec: pyvcf
- helper scripts for Variant Call Format (VCF) parser
-
- rec: qcat
- demultiplexing Oxford Nanopore reads from FASTQ files
-
- rec: qcumber
- quality control of genomic sequences
-
- rec: qiime
- Quantitative Insights Into Microbial Ecology
-
- rec: qtltools
- Tool set for molecular QTL discovery and analysis
-
- rec: quicktree
- Neighbor-Joining algorithm for phylogenies
-
- rec: quorum
- QUality Optimized Reads of genomic sequences
-
- rec: qutemol
- interactive visualization of macromolecules
-
- rec: r-bioc-annotate
- BioConductor annotation for microarrays
-
- rec: r-bioc-biostrings
- GNU R string objects representing biological sequences
-
- rec: r-bioc-cner
- CNE Detection and Visualization
-
- rec: r-bioc-cummerbund
- tool for analysis of Cufflinks RNA-Seq output
-
- rec: r-bioc-deseq2
- R package for RNA-Seq Differential Expression Analysis
-
- rec: r-bioc-ebseq
- R package for RNA-Seq Differential Expression Analysis
-
- rec: r-bioc-edger
- Empirical analysis of digital gene expression data in R
-
- rec: r-bioc-genefilter
- methods for filtering genes from microarray experiments
-
- rec: r-bioc-geoquery
- Get data from NCBI Gene Expression Omnibus (GEO)
-
- rec: r-bioc-hilbertvis
- GNU R package to visualise long vector data
-
- rec: r-bioc-htsfilter
- GNU R filter replicated high-throughput transcriptome sequencing data
-
- rec: r-bioc-impute
- Imputation for microarray data
-
- rec: r-bioc-limma
- linear models for microarray data
-
- rec: r-bioc-megadepth
- BioCOnductor BigWig and BAM related utilities
-
- rec: r-bioc-mergeomics
- Integrative network analysis of omics data
-
- rec: r-bioc-metagenomeseq
- GNU R statistical analysis for sparse high-throughput sequencing
-
- rec: r-bioc-mofa
- Multi-Omics Factor Analysis (MOFA)
-
- rec: r-bioc-multiassayexperiment
- Software for integrating multi-omics experiments in BioConductor
-
- rec: r-bioc-mutationalpatterns
- GNU R comprehensive genome-wide analysis of mutational processes
-
- rec: r-bioc-pcamethods
- BioConductor collection of PCA methods
-
- rec: r-bioc-phyloseq
- GNU R handling and analysis of high-throughput microbiome census data
-
- rec: r-bioc-rtracklayer
- GNU R interface to genome browsers and their annotation tracks
-
- rec: r-bioc-scater
- Single-Cell Analysis Toolkit for Gene Expression Data in R
-
- rec: r-bioc-tfbstools
- GNU R Transcription Factor Binding Site (TFBS) Analysis
-
- rec: r-cran-adegenet
- GNU R exploratory analysis of genetic and genomic data
-
- rec: r-cran-adephylo
- GNU R exploratory analyses for the phylogenetic comparative method
-
- rec: r-cran-alakazam
- Immunoglobulin Clonal Lineage and Diversity Analysis
-
- rec: r-cran-ape
- GNU R package for Analyses of Phylogenetics and Evolution
-
- rec: r-cran-bio3d
- GNU R package for biological structure analysis
-
- rec: r-cran-distory
- GNU R distance between phylogenetic histories
-
- rec: r-cran-genabel
- GNU R package for genome-wide SNP association analysis
-
- rec: r-cran-kaos
- Encoding of Sequences Based on Frequency Matrix Chaos
-
- rec: r-cran-metamix
- GNU R bayesian mixture analysis for metagenomic community profiling
-
- rec: r-cran-phangorn
- GNU R package for phylogenetic analysis
-
- rec: r-cran-phytools
- GNU R phylogenetic tools for comparative biology
-
- rec: r-cran-pscbs
- R package: Analysis of Parent-Specific DNA Copy Numbers
-
- rec: r-cran-qtl
- GNU R package for genetic marker linkage analysis
-
- rec: r-cran-rotl
- GNU R interface to the 'Open Tree of Life' API
-
- rec: r-cran-samr
- GNU R significance analysis of microarrays
-
- rec: r-cran-sdmtools
- Species Distribution Modelling Tools
-
- rec: r-cran-seqinr
- GNU R biological sequences retrieval and analysis
-
- rec: r-cran-seurat
- Tools for Single Cell Genomics
-
- rec: r-cran-shazam
- Immunoglobulin Somatic Hypermutation Analysis
-
- rec: r-cran-spp
- GNU R ChIP-seq processing pipeline
-
- rec: r-cran-tcr
- Advanced Data Analysis of Immune Receptor Repertoires
-
- rec: r-cran-tigger
- Infers new Immunoglobulin alleles from Rep-Seq Data
-
- rec: r-cran-treescape
- 套件暫時不可用
-
- rec: r-cran-tsne
- t-distributed stochastic neighbor embedding for R (t-SNE)
-
- rec: r-cran-vegan
- Community Ecology Package for R
-
- rec: r-cran-webgestaltr
- find over-represented properties in gene lists
-
- rec: r-cran-wgcna
- Weighted Correlation Network Analysis
-
- rec: r-other-ascat
- Allele-Specific Copy Number Analysis of Tumours
-
- rec: r-other-mott-happy.hbrem
- GNU R package for fine-mapping complex diseases
-
- rec: r-other-rajewsky-dropbead
- Basic Exploration and Analysis of Drop-seq Data
-
- rec: racon
- consensus module for raw de novo DNA assembly of long uncorrected reads
-
- rec: radiant
- explore hierarchical metagenomic data with zoomable pie charts
-
- rec: ragout
- Reference-Assisted Genome Ordering UTility
-
- rec: rambo-k
- Read Assignment Method Based On K-mers
-
- rec: rampler
- module for sampling genomic sequences
-
- rec: rapmap
- rapid sensitive and accurate DNA read mapping via quasi-mapping
-
- rec: rasmol
- visualization of biological macromolecules
-
- rec: raster3d
- tools for generating images of proteins or other molecules
-
- rec: rate4site
- detector of conserved amino-acid sites
-
- rec: raxml
- Randomized Axelerated Maximum Likelihood of phylogenetic trees
-
- rec: ray
- de novo genome assemblies of next-gen sequencing data
-
- rec: rdp-alignment
- Ribosomal Database Project (RDP) alignment tools package
-
- rec: rdp-classifier
- extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
-
- rec: rdp-readseq
- Ribosomal Database Project (RDP) sequence reading and writing
-
- rec: readseq
- Conversion between sequence formats
-
- rec: readucks
- Nanopore read de-multiplexer (read demux -> readux -> readucks, innit)
-
- rec: reapr
- universal tool for genome assembly evaluation
-
- rec: recan
- genetic distance plotting for recombination events analysis
-
- rec: relion
- toolkit for 3D reconstructions in cryo-electron microscopy
-
- rec: relion-gui
- toolkit for 3D reconstructions in cryo-electron microscopy (gui apps)
-
- rec: repeatmasker-recon
- finds repeat families from biological sequences
-
- rec: reprof
- protein secondary structure and accessibility predictor
-
- rec: resfinder
- identify acquired antimicrobial resistance genes
-
- rec: rna-star
- ultrafast universal RNA-seq aligner
-
- rec: rnahybrid
- Fast and effective prediction of microRNA/target duplexes
-
- rec: roary
- high speed stand alone pan genome pipeline
-
- rec: rockhopper
- system for analyzing bacterial RNA-seq data
-
- rec: roguenarok
- versatile and scalable algorithm for rogue taxon identification
-
- rec: rsem
- RNA-Seq by Expectation-Maximization
-
- rec: rtax
- Classification of sequence reads of 16S ribosomal RNA gene
-
- rec: runcircos-gui
- GUI tool to run circos
-
- rec: saint
- Significance Analysis of INTeractome
-
- rec: salmid
- rapid Kmer based Salmonella identifier from sequence data
-
- rec: salmon
- wicked-fast transcript quantification from RNA-seq data
-
- rec: sambamba
- tools for working with SAM/BAM data
-
- rec: samblaster
- marks duplicates, extracts discordant/split reads
-
- rec: samclip
- filter SAM file for soft and hard clipped alignments
-
- rec: samtools
- processing sequence alignments in SAM, BAM and CRAM formats
-
- rec: savvy-util
- conversion tool for SAV file format
-
- rec: scoary
- pangenome-wide association studies
-
- rec: scrappie
- basecaller for Nanopore sequencer
-
- rec: scrm
- simulator of evolution of genetic sequences
-
- rec: scythe
- Bayesian adaptor trimmer for sequencing reads
-
- rec: seaview
- Multiplatform interface for sequence alignment and phylogeny
-
- rec: seer
- genomic sequence element (kmer) enrichment analysis
-
- rec: segemehl
- short read mapping with gaps
-
- rec: seqan-apps
- C++ library for the analysis of biological sequences
-
- rec: seqan-needle
- pre-filter for the counting of very large collections of nucleotide sequences
-
- rec: seqan-raptor
- pre-filter for querying very large collections of nucleotide sequences
-
- rec: seqkit
- cross-platform and ultrafast toolkit for FASTA/Q file manipulation
-
- rec: seqmagick
- imagemagick-like frontend to Biopython SeqIO
-
- rec: seqprep
- stripping adaptors and/or merging paired reads of DNA sequences with overlap
-
- rec: seqsero
- Salmonella serotyping from genome sequencing data
-
- rec: seqtk
- Fast and lightweight tool for processing sequences in the FASTA or FASTQ format
-
- rec: sga
- de novo genome assembler that uses string graphs
-
- rec: shasta
- nanopore whole genome assembly (binaries and scripts)
-
- rec: shovill
- Assemble bacterial isolate genomes from Illumina paired-end reads
-
- rec: sibelia
- comparative genomics tool
-
- rec: sibsim4
- align expressed RNA sequences on a DNA template
-
- rec: sickle
- windowed adaptive trimming tool for FASTQ files using quality
-
- rec: sigma-align
- Simple greedy multiple alignment of non-coding DNA sequences
-
- rec: sim4
- tool for aligning cDNA and genomic DNA
-
- rec: sim4db
- batch spliced alignment of cDNA sequences to a target genome
-
- rec: simka
- comparative metagenomics method dedicated to NGS datasets
-
- rec: simkamin
- approximate comparative metagenomics method dedicated to NGS datasets
-
- rec: ska
- Split Kmer Analysis
-
- rec: skesa
- strategic Kmer extension for scrupulous assemblies
-
- rec: skewer
- post-processing of high-throughput DNA sequence reads
-
- rec: smalt
- Sequence Mapping and Alignment Tool
-
- rec: smithwaterman
- determine similar regions between two strings or genomic sequences
-
- rec: smrtanalysis
- software suite for single molecule, real-time sequencing
-
- rec: snap
- location of genes from DNA sequence with hidden markov model
-
- rec: snap-aligner
- Scalable Nucleotide Alignment Program
-
- rec: sniffles
- structural variation caller using third-generation sequencing
-
- rec: snp-sites
- Binary code for the package snp-sites
-
- rec: snpeff
- genetic variant annotation and effect prediction toolbox - tool
-
- rec: snpomatic
- fast, stringent short-read mapping software
-
- rec: snpsift
- tool to annotate and manipulate genome variants - tool
-
- rec: soapaligner
- aligner of short reads of next generation sequencers
-
- rec: soapdenovo
- short-read assembly method to build de novo draft assembly
-
- rec: soapdenovo2
- short-read assembly method to build de novo draft assembly
-
- rec: soapsnp
- resequencing utility that can assemble consensus sequence of genomes
-
- rec: sortmerna
- tool for filtering, mapping and OTU-picking NGS reads
-
- rec: spaced
- alignment-free sequence comparison using spaced words
-
- rec: spades
- genome assembler for single-cell and isolates data sets
-
- rec: spaln
- splicing-aware transcript-alignment to genomic DNA
-
- rec: spoa
- SIMD partial order alignment tool
-
- rec: sprai
- single-pass sequencing read accuracy improver
-
- rec: spread-phy
- analyze and visualize phylogeographic reconstructions
-
- rec: squizz
- Converter for genetic sequences and alignments
-
- rec: sra-toolkit
- utilities for the NCBI Sequence Read Archive
-
- rec: srst2
- Short Read Sequence Typing for Bacterial Pathogens
-
- rec: ssake
- genomics application for assembling millions of very short DNA sequences
-
- rec: sspace
- scaffolding pre-assembled contigs after extension
-
- rec: ssw-align
- Smith-Waterman aligner based on libssw
-
- rec: stacks
- pipeline for building loci from short-read DNA sequences
-
- rec: staden
- DNA sequence assembly (Gap4/Gap5), editing and analysis tools
-
- rec: staden-io-lib-utils
- programs for manipulating DNA sequencing files
-
- rec: stringtie
- assemble short RNAseq reads to transcripts
-
- rec: subread
- toolkit for processing next-gen sequencing data
-
- rec: suitename
- categorize each suite in an RNA backbone
-
- rec: sumaclust
- fast and exact clustering of genomic sequences
-
- rec: sumatra
- fast and exact comparison and clustering of sequences
-
- rec: sumtrees
- Phylogenetic Tree Summarization and Annotation
-
- rec: surankco
- Supervised Ranking of Contigs in de novo Assemblies
-
- rec: surpyvor
- modification of VCF files with SURVIVOR
-
- rec: survivor
- tool set for simulating/evaluating SVs
-
- rec: svim
- Structural variant caller for long sequencing reads
-
- rec: swarm
- robust and fast clustering method for amplicon-based studies
-
- rec: sweed
- assessment of SNPs for their evolutionary advantage
-
- rec: t-coffee
- Multiple Sequence Alignment
-
- rec: tabix
- generic indexer for TAB-delimited genome position files
-
- rec: tantan
- low complexity and tandem repeat masker for biosequences
-
- rec: terraphast
- enumerate terraces in phylogenetic tree space
-
- rec: theseus
- superimpose macromolecules using maximum likelihood
-
- rec: thesias
- Testing Haplotype Effects In Association Studies
-
- rec: tiddit
- structural variant calling
-
- rec: tigr-glimmer
- Gene detection in archea and bacteria
-
- rec: tm-align
- structural alignment of proteins
-
- rec: tnseq-transit
- statistical calculations of essentiality of genes or genomic regions
-
- rec: toil
- cross-platform workflow engine
-
- rec: tombo
- identification of modified nucleotides from raw nanopore sequencing data
-
- rec: tophat-recondition
- post-processor for TopHat unmapped reads
-
- rec: topp
- set of programs implementing The OpenMS Proteomic Pipeline
-
- rec: toppred
- transmembrane topology prediction
-
- rec: tortoize
- Application to calculate ramachandran z-scores
-
- rec: trace2dbest
- bulk submission of chromatogram data to dbEST
-
- rec: tracetuner
- interpretation of DNA Sanger sequencing data
-
- rec: transdecoder
- find coding regions within RNA transcript sequences
-
- rec: transrate-tools
- helper for transrate
-
- rec: transtermhp
- find rho-independent transcription terminators in bacterial genomes
-
- rec: tree-puzzle
- Reconstruction of phylogenetic trees by maximum likelihood
- 或者 tree-ppuzzle
- Parallelized reconstruction of phylogenetic trees by maximum likelihood
-
- rec: treeview
- Java re-implementation of Michael Eisen's TreeView
-
- rec: treeviewx
- Displays and prints phylogenetic trees
-
- rec: trf
- locate and display tandem repeats in DNA sequences
-
- rec: trim-galore
- automate quality and adapter trimming for DNA sequencing
-
- rec: trimmomatic
- flexible read trimming tool for Illumina NGS data
-
- rec: tvc
- genetic variant caller for Ion Torrent sequencing platforms
-
- rec: twopaco
- build the compacted de Bruijn graph from many complete genomes
-
- rec: uc-echo
- error correction algorithm designed for short-reads from NGS
-
- rec: umap-learn
- Uniform Manifold Approximation and Projection
-
- rec: umis
- tools for processing UMI RNA-tag data
-
- rec: uncalled
- Utility for Nanopore Current Alignment to Large Expanses of DNA
-
- rec: unicycler
- hybrid assembly pipeline for bacterial genomes
-
- rec: unikmer
- Toolkit for nucleic acid k-mer analysis
-
- rec: varna
- Visualization Applet for RNA
-
- rec: vcfanno
- annotate a VCF with other VCFs/BEDs/tabixed files
-
- rec: vcftools
- Collection of tools to work with VCF files
-
- rec: velvet
- Nucleic acid sequence assembler for very short reads
- 或者 velvet-long
- Nucleic acid sequence assembler for very short reads, long version
-
- rec: velvetoptimiser
- automatically optimise Velvet do novo assembly parameters
-
- rec: virulencefinder
- identify virulence genes in total or partial sequenced isolates of bacteria
-
- rec: vmatch
- large scale sequence analysis software
-
- rec: vsearch
- tool for processing metagenomic sequences
-
- rec: vt
- toolset for short variant discovery in genetic sequence data
-
- rec: wham-align
- Wisconsin's High-Throughput Alignment Method
-
- rec: wigeon
- reimplementation of the Pintail 16S DNA anomaly detection utility
-
- rec: wise
- comparison of biopolymers, like DNA and protein sequences
-
- rec: xpore
- Nanopore analysis of differential RNA modifications
-
- rec: yaha
- find split-read mappings on single-end queries
-
- rec: yanagiba
- filter low quality Oxford Nanopore reads basecalled with Albacore
-
- rec: yanosim
- read simulator nanopore DRS datasets
-
- sug: acacia
- 套件暫時不可用
-
- sug: adun.app
- Molecular Simulator for GNUstep (GUI)
-
- sug: agat
- 套件暫時不可用
-
- sug: amos-assembler
- 套件暫時不可用
-
- sug: amoscmp
- 套件暫時不可用
-
- sug: anfo
- Short Read Aligner/Mapper from MPG
-
- sug: annovar
- 套件暫時不可用
-
- sug: apollo
- 套件暫時不可用
-
- sug: arachne
- 套件暫時不可用
-
- sug: arb
- phylogenetic sequence analysis suite - main program
-
- sug: arvados
- 套件暫時不可用
-
- sug: asap
- 套件暫時不可用
-
- sug: axparafit
- 套件暫時不可用
-
- sug: axpcoords
- 套件暫時不可用
-
- sug: bagpipe
- 套件暫時不可用
-
- sug: bambus
- 套件暫時不可用
-
- sug: bax2bam
- 套件暫時不可用
-
- sug: bcbio
- toolkit for analysing high-throughput sequencing data
-
- sug: biceps
- 套件暫時不可用
-
- sug: big-blast
- 套件暫時不可用
-
- sug: bigsdb
- 套件暫時不可用
-
- sug: bismark
- 套件暫時不可用
-
- sug: blat
- 套件暫時不可用
-
- sug: blimps-utils
- blocks database improved searcher
-
- sug: blobology
- 套件暫時不可用
-
- sug: braker
- 套件暫時不可用
-
- sug: btk-core
- 套件暫時不可用
-
- sug: cactus
- 套件暫時不可用
-
- sug: caftools
- 套件暫時不可用
-
- sug: card-rgi
- 套件暫時不可用
-
- sug: catfishq
- concatenates fastq files
-
- sug: cdna-db
- 套件暫時不可用
-
- sug: cellprofiler
- 套件暫時不可用
-
- sug: cinema
- 套件暫時不可用
-
- sug: cluster3
- Reimplementation of the Eisen-clustering software
-
- sug: cmap
- 套件暫時不可用
-
- sug: conda-package-handling
- create and extract conda packages of various formats
-
- sug: condetri
- 套件暫時不可用
-
- sug: contrafold
- 套件暫時不可用
-
- sug: contralign
- 套件暫時不可用
-
- sug: coot
- model building program for macromolecular crystallography
-
- sug: copycat
- 套件暫時不可用
-
- sug: covpipe
- 套件暫時不可用
-
- sug: crossbow
- 套件暫時不可用
-
- sug: crux-toolkit
- 套件暫時不可用
-
- sug: cufflinks
- Transcript assembly, differential expression and regulation for RNA-Seq
-
- sug: cytoscape
- 套件暫時不可用
-
- sug: dascrubber
- alignment-based scrubbing pipeline for DNA sequencing reads
-
- sug: dazzle
- 套件暫時不可用
-
- sug: deepbinner
- 套件暫時不可用
-
- sug: deepnano
- 套件暫時不可用
-
- sug: dendroscope
- 套件暫時不可用
-
- sug: diann
- 套件暫時不可用
-
- sug: dnapi
- adapter prediction for small RNA sequencing - utils
-
- sug: e-hive
- 套件暫時不可用
-
- sug: ecell
- 套件暫時不可用
-
- sug: embassy-phylip
- 套件暫時不可用
-
- sug: emboss-explorer
- web-based GUI to EMBOSS
-
- sug: ensembl
- 套件暫時不可用
-
- sug: ensembl-vep
- 套件暫時不可用
-
- sug: epigrass
- scientific tool for simulations and scenario analysis in network epidemiology
-
- sug: estferret
- 套件暫時不可用
-
- sug: euler-sr
- 套件暫時不可用
-
- sug: euler2
- 套件暫時不可用
-
- sug: exabayes
- 套件暫時不可用
-
- sug: exalt
- 套件暫時不可用
-
- sug: excavator
- 套件暫時不可用
-
- sug: ffp
- 套件暫時不可用
-
- sug: fieldbioinformatics
- 套件暫時不可用
-
- sug: figaro
- 套件暫時不可用
-
- sug: flappie
- 套件暫時不可用
-
- sug: forester
- 套件暫時不可用
-
- sug: forge
- 套件暫時不可用
-
- sug: galaxy
- 套件暫時不可用
-
- sug: gatk
- 套件暫時不可用
-
- sug: gbrowse-syn
- 套件暫時不可用
-
- sug: genemark
- 套件暫時不可用
-
- sug: genesplicer
- 套件暫時不可用
-
- sug: genetrack
- 套件暫時不可用
-
- sug: genezilla
- 套件暫時不可用
-
- sug: genographer
- 套件暫時不可用
-
- sug: gerp++
- 套件暫時不可用
-
- sug: getdata
- management of external databases
-
- sug: glimmerhmm
- 套件暫時不可用
-
- sug: gmv
- 套件暫時不可用
-
- sug: gramalign
- 套件暫時不可用
-
- sug: graphbin
- 套件暫時不可用
-
- sug: graphmap2
- 套件暫時不可用
-
- sug: haploview
- 套件暫時不可用
-
- sug: hawkeye
- 套件暫時不可用
-
- sug: htqc
- 套件暫時不可用
-
- sug: hts-nim-tools
- tools biological sequences: bam-filter, count-reads, vcf-check
-
- sug: idefix
- 套件暫時不可用
-
- sug: idseq-bench
- Benchmark generator for the IDseq Portal
-
- sug: igdiscover
- analyzes antibody repertoires to find new V genes
-
- sug: illustrate
- cartoonish representations of large biological molecules
-
- sug: inspect
- 套件暫時不可用
-
- sug: jbrowse
- 套件暫時不可用
-
- sug: jigsaw
- 套件暫時不可用
-
- sug: kempbasu
- 套件暫時不可用
-
- sug: libhdf5-dev
- HDF5 - development files - serial version
-
- sug: libhnswlib-dev
- fast approximate nearest neighbor search
-
- sug: lofreq
- 套件暫時不可用
-
- sug: mach-haplotyper
- 套件暫時不可用
-
- sug: mage2tab
- 套件暫時不可用
-
- sug: maker2
- 套件暫時不可用
-
- sug: manta
- 套件暫時不可用
-
- sug: marginphase
- 套件暫時不可用
-
- sug: martj
- 套件暫時不可用
-
- sug: maude
- high-performance logical framework
-
- sug: maxd
- 套件暫時不可用
-
- sug: medaka
- 套件暫時不可用
-
- sug: meme
- 套件暫時不可用
-
- sug: mesquite
- 套件暫時不可用
-
- sug: metabit
- 套件暫時不可用
-
- sug: metaeuk
- sensitive, high-throughput gene discovery and annotation for metagenomics
-
- sug: metarep
- 套件暫時不可用
-
- sug: metastudent-data
- predictor of Gene Ontology terms from protein sequence - data files
-
- sug: metastudent-data-2
- predictor of Gene Ontology terms from protein sequence - data #2
-
- sug: migrate
- 套件暫時不可用
-
- sug: minimus
- 套件暫時不可用
-
- sug: mirbase
- 套件暫時不可用
-
- sug: modeller
- 套件暫時不可用
-
- sug: molekel
- 套件暫時不可用
-
- sug: mosaik-aligner
- 套件暫時不可用
-
- sug: mpsqed
- 套件暫時不可用
-
- sug: mrs
- 套件暫時不可用
-
- sug: msatfinder
- 套件暫時不可用
-
- sug: mugsy
- 套件暫時不可用
-
- sug: mummergpu
- 套件暫時不可用
-
- sug: mview
- 套件暫時不可用
-
- sug: nano-snakemake
- 套件暫時不可用
-
- sug: nanocall
- 套件暫時不可用
-
- sug: nanocomp
- 套件暫時不可用
-
- sug: nanoplot
- 套件暫時不可用
-
- sug: ncbi-magicblast
- 套件暫時不可用
-
- sug: nextsv
- 套件暫時不可用
-
- sug: ngila
- 套件暫時不可用
-
- sug: ngsqctoolkit
- 套件暫時不可用
-
- sug: nw-align
- 套件暫時不可用
-
- sug: oases
- 套件暫時不可用
-
- sug: obo-edit
- 套件暫時不可用
-
- sug: oligoarrayaux
- 套件暫時不可用
-
- sug: omegamap
- 套件暫時不可用
-
- sug: oncofuse
- 套件暫時不可用
-
- sug: operondb
- 套件暫時不可用
-
- sug: optitype
- 套件暫時不可用
-
- sug: paipline
- 套件暫時不可用
-
- sug: pangolin
- 套件暫時不可用
-
- sug: partigene
- 套件暫時不可用
-
- sug: partitionfinder
- 套件暫時不可用
-
- sug: patristic
- 套件暫時不可用
-
- sug: pcma
- 套件暫時不可用
-
- sug: pfaat
- 套件暫時不可用
-
- sug: phagefinder
- 套件暫時不可用
-
- sug: phpphylotree
- 套件暫時不可用
-
- sug: phylographer
- 套件暫時不可用
-
- sug: phylophlan
- 套件暫時不可用
-
- sug: phyloviz-core
- 套件暫時不可用
-
- sug: phylowin
- 套件暫時不可用
-
- sug: pigx-scrnaseq
- 套件暫時不可用
-
- sug: pipasic
- 套件暫時不可用
-
- sug: plato
- 套件暫時不可用
-
- sug: pomoxis
- 套件暫時不可用
-
- sug: pplacer
- phylogenetic placement and downstream analysis
-
- sug: profit
- 套件暫時不可用
-
- sug: profphd
- 套件暫時不可用
-
- sug: prot4est
- 套件暫時不可用
-
- sug: psipred
- 套件暫時不可用
-
- sug: pssh2
- 套件暫時不可用
-
- sug: pufferfish
- 套件暫時不可用
-
- sug: purple
- 套件暫時不可用
-
- sug: pyrophosphate-tools
- 套件暫時不可用
-
- sug: python3-alignlib
- edit and Hamming distances for biological sequences
-
- sug: python3-anndata
- annotated gene by sample numpy matrix
-
- sug: python3-cgecore
- Python3 module for the Center for Genomic Epidemiology
-
- sug: python3-cyvcf2
- VCF parser based on htslib (Python 3)
-
- sug: python3-deeptools
- platform for exploring biological deep-sequencing data
-
- sug: python3-deeptoolsintervals
- handlig GTF-like sequence-associated interal-annotation
-
- sug: python3-htseq
- Python3 high-throughput genome sequencing read analysis utilities
-
- sug: python3-intake
- lightweight package for finding and investigating data
-
- sug: python3-loompy
- access loom formatted files for bioinformatics
-
- sug: python3-nanoget
- extract information from Oxford Nanopore sequencing data and alignments
-
- sug: python3-nanomath
- simple math function for other Oxford Nanopore processing scripts
-
- sug: python3-ncls
- datastructure for interval overlap queries
-
- sug: python3-orange
- 套件暫時不可用
-
- sug: python3-py2bit
- access to 2bit files
-
- sug: python3-pybel
- Biological Expression Language
-
- sug: python3-pychopper
- identify, orient and trim full-length Nanopore cDNA reads
-
- sug: python3-pyfaidx
- efficient random access to fasta subsequences for Python 3
-
- sug: python3-pyflow
- lightweight parallel task engine for Python
-
- sug: python3-pyranges
- 2D representation of genomic intervals and their annotations
-
- sug: python3-pyrle
- run length arithmetic in Python
-
- sug: python3-pysam
- interface for the SAM/BAM sequence alignment and mapping format (Python 3)
-
- sug: python3-tinyalign
- numerical representation of differences between strings
-
- sug: q2-alignment
- QIIME 2 plugin for generating and manipulating alignments
-
- sug: q2-composition
- 套件暫時不可用
-
- sug: q2-cutadapt
- QIIME 2 plugin to work with adapters in sequence data
-
- sug: q2-dada2
- QIIME 2 plugin to work with adapters in sequence data
-
- sug: q2-deblur
- 套件暫時不可用
-
- sug: q2-demux
- QIIME 2 plugin for demultiplexing of sequence reads
-
- sug: q2-diversity
- 套件暫時不可用
-
- sug: q2-emperor
- QIIME2 plugin for display of ordination plots
-
- sug: q2-feature-classifier
- QIIME 2 plugin supporting taxonomic classification
-
- sug: q2-feature-table
- QIIME 2 plugin supporting operations on feature tables
-
- sug: q2-fragment-insertion
- QIIME 2 plugin for fragment insertion
-
- sug: q2-gneiss
- 套件暫時不可用
-
- sug: q2-longitudinal
- 套件暫時不可用
-
- sug: q2-metadata
- QIIME 2 plugin for working with and visualizing Metadata
-
- sug: q2-phylogeny
- QIIME 2 plugin for phylogeny
-
- sug: q2-quality-control
- QIIME 2 plugin for quality assurance of feature and sequence data
-
- sug: q2-quality-filter
- QIIME2 plugin for PHRED-based filtering and trimming
-
- sug: q2-sample-classifier
- QIIME 2 plugin for machine learning prediction of sample data
-
- sug: q2-taxa
- QIIME 2 plugin for working with feature taxonomy annotations
-
- sug: q2-types
- QIIME 2 plugin defining types for microbiome analysis
-
- sug: q2-vsearch
- 套件暫時不可用
-
- sug: q2cli
- Click-based command line interface for QIIME 2
-
- sug: q2templates
- Design template package for QIIME 2 Plugins
-
- sug: qtlcart
- 套件暫時不可用
-
- sug: qtlreaper
- 套件暫時不可用
-
- sug: qualimap
- 套件暫時不可用
-
- sug: quast
- 套件暫時不可用
-
- sug: r-bioc-annotationhub
- GNU R client to access AnnotationHub resources
-
- sug: r-bioc-aroma.light
- BioConductor methods normalization and visualization of microarray data
-
- sug: r-bioc-beachmat
- I/O for several formats storing matrix data
-
- sug: r-bioc-biocneighbors
- Nearest Neighbor Detection for Bioconductor Packages
-
- sug: r-bioc-biocsingular
- Singular Value Decomposition for Bioconductor Packages
-
- sug: r-bioc-bitseq
- 套件暫時不可用
-
- sug: r-bioc-ctc
- Cluster and Tree Conversion
-
- sug: r-bioc-dnacopy
- R package: DNA copy number data analysis
-
- sug: r-bioc-ensembldb
- GNU R utilities to create and use an Ensembl based annotation database
-
- sug: r-bioc-experimenthub
- BioConductor client to access ExperimentHub resources
-
- sug: r-bioc-geneplotter
- R package of functions for plotting genomic data
-
- sug: r-bioc-genomicalignments
- BioConductor representation and manipulation of short genomic alignments
-
- sug: r-bioc-genomicfiles
- Distributed computing by file or by range
-
- sug: r-bioc-genomicranges
- BioConductor representation and manipulation of genomic intervals
-
- sug: r-bioc-go.db
- annotation maps describing the entire Gene Ontology
-
- sug: r-bioc-grohmm
- GRO-seq Analysis Pipeline
-
- sug: r-bioc-gviz
- Plotting data and annotation information along genomic coordinates
-
- sug: r-bioc-isoformswitchanalyzer
- Identify, Annotate and Visualize Alternative Splicing and
-
- sug: r-bioc-mofa2
- 套件暫時不可用
-
- sug: r-bioc-org.hs.eg.db
- genome-wide annotation for Human
-
- sug: r-bioc-org.mm.eg.db
- 套件暫時不可用
-
- sug: r-bioc-qusage
- qusage: Quantitative Set Analysis for Gene Expression
-
- sug: r-bioc-savr
- GNU R parse and analyze Illumina SAV files
-
- sug: r-bioc-singlecellexperiment
- S4 Classes for Single Cell Data
-
- sug: r-bioc-structuralvariantannotation
- Variant annotations for structural variants
-
- sug: r-bioc-tximport
- transcript-level estimates for biological sequencing
-
- sug: r-cran-amap
- Another Multidimensional Analysis Package
-
- sug: r-cran-biwt
- biweight mean vector and covariance and correlation
-
- sug: r-cran-boolnet
- assembling, analyzing and visualizing Boolean networks
-
- sug: r-cran-corrplot
- Visualization of a Correlation Matrix
-
- sug: r-cran-drinsight
- 套件暫時不可用
-
- sug: r-cran-dynamictreecut
- Methods for Detection of Clusters in Hierarchical Clustering
-
- sug: r-cran-epir
- GNU R Functions for analysing epidemiological data
-
- sug: r-cran-fitdistrplus
- support fit of parametric distribution
-
- sug: r-cran-forecast
- GNU R forecasting functions for time series and linear models
-
- sug: r-cran-gprofiler2
- Interface to the 'g:Profiler' Toolset
-
- sug: r-cran-minerva
- Maximal Information-Based Nonparametric Exploration
-
- sug: r-cran-optimalcutpoints
- Computing Optimal Cutpoints in Diagnostic Tests
-
- sug: r-cran-parmigene
- Parallel Mutual Information to establish Gene Networks
-
- sug: r-cran-pheatmap
- GNU R package to create pretty heatmaps
-
- sug: r-cran-qqman
- R package for visualizing GWAS results using Q-Q and manhattan plots
-
- sug: r-cran-rcpphnsw
- R bindings for a Library for Approximate Nearest Neighbors
-
- sug: r-cran-rentrez
- GNU R interface to the NCBI's EUtils API
-
- sug: r-cran-sctransform
- Variance Stabilizing Transformations for Single Cell UMI Data
-
- sug: r-other-apmswapp
- 套件暫時不可用
-
- sug: r-other-fastbaps
- 套件暫時不可用
-
- sug: raccoon
- 套件暫時不可用
-
- sug: raxml-ng
- 套件暫時不可用
-
- sug: rbs-finder
- 套件暫時不可用
-
- sug: relion-cuda
- parallel toolkit for 3D reconstructions in cryo-electron microscopy
-
- sug: relion-gui-cuda
- toolkit for 3D reconstructions in cryo-electron microscopy (gui apps)
-
- sug: repeatmasker
- 套件暫時不可用
-
- sug: resfinder-db
- ResFinder database is a curated database of acquired resistance genes
-
- sug: roadtrips
- 套件暫時不可用
-
- sug: roche454ace2caf
- 套件暫時不可用
-
- sug: rosa
- 套件暫時不可用
-
- sug: rose
- 套件暫時不可用
-
- sug: rsat
- 套件暫時不可用
-
- sug: sailfish
- 套件暫時不可用
-
- sug: sap
- 套件暫時不可用
-
- sug: science-workflow
- workflow management systems useful for scientific research
-
- sug: sepp
- phylogeny with ensembles of Hidden Markov Models
-
- sug: seq-gen
- simulate the evolution of nucleotide or amino acid sequences
-
- sug: seq-seq-pan
- 套件暫時不可用
-
- sug: seqcluster
- analysis of small RNA in NGS data
-
- sug: seqwish
- 套件暫時不可用
-
- sug: sift
- predicts if a substitution in a protein has a phenotypic effect
-
- sug: signalalign
- 套件暫時不可用
-
- sug: sina
- 套件暫時不可用
-
- sug: sistr
- 套件暫時不可用
-
- sug: situs
- 套件暫時不可用
-
- sug: snippy
- rapid haploid variant calling and core genome alignment
-
- sug: solvate
- arranges water molecules around protein structures
-
- sug: sourmash
- 套件暫時不可用
-
- sug: sparta
- 套件暫時不可用
-
- sug: splitstree
- 套件暫時不可用
-
- sug: ssaha
- 套件暫時不可用
-
- sug: strap
- 套件暫時不可用
-
- sug: strap-base
- 套件暫時不可用
-
- sug: strelka
- 套件暫時不可用
-
- sug: tab2mage
- 套件暫時不可用
-
- sug: tacg
- 套件暫時不可用
-
- sug: tandem-genotypes
- 套件暫時不可用
-
- sug: taverna
- 套件暫時不可用
-
- sug: taxinspector
- 套件暫時不可用
-
- sug: tetra
- 套件暫時不可用
-
- sug: tide
- 套件暫時不可用
-
- sug: tigr-glimmer-mg
- 套件暫時不可用
-
- sug: tipp
- tool for Taxonomic Identification and Phylogenetic Profiling
-
- sug: tn-seqexplorer
- 套件暫時不可用
-
- sug: tophat
- 套件暫時不可用
-
- sug: treebuilder3d
- 套件暫時不可用
-
- sug: trinityrnaseq
- RNA-Seq De novo Assembly
-
- sug: tripal
- 套件暫時不可用
-
- sug: trnascan-se
- detection of transfer RNA genes in genomic sequence
-
- sug: twain
- 套件暫時不可用
-
- sug: ufasta
- 套件暫時不可用
-
- sug: ugene
- integrated bioinformatics toolkit
-
- sug: umap
- 套件暫時不可用
-
- sug: unc-fish
- 套件暫時不可用
-
- sug: uniprime
- 套件暫時不可用
-
- sug: varmatch
- 套件暫時不可用
-
- sug: varscan
- variant detection in next-generation sequencing data
-
- sug: vdjtools
- framework for post-analysis of B/T cell repertoires
-
- sug: vg
- tools for working with genome variation graphs
-
- sug: vienna-rna
- RNA sequence analysis
-
- sug: viewmol
- 套件暫時不可用
-
- sug: vmd
- 套件暫時不可用
-
- sug: x-tandem-pipeline
- 套件暫時不可用
-
- sug: zodiac-zeden
- 套件暫時不可用