[ ソース: debian-med ]
パッケージ: med-bio (3.3)
Debian Med bioinformatics packages
This metapackage will install Debian packages for use in molecular biology, structural biology and other biological sciences.
その他の med-bio 関連パッケージ
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- dep: med-config (= 3.3)
- Debian Med general config package
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- dep: med-tasks (= 3.3)
- Debian Med tasks for tasksel
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- rec: abacas
- close gaps in genomic alignments from short reads
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- rec: abyss
- de novo, parallel, sequence assembler for short reads
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- rec: acedb-other
- DNA およびタンパク質配列の取得
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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
- 水平伝播 DNA を識別するための Interpolated Variable Order Motifs
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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: anfo
- Short Read Aligner/Mapper from MPG
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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: 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: augustus
- gene prediction in eukaryotic genomes
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- rec: autodock
- タンパク質構造に結合するリガンドの分析ツール
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- rec: autodock-vina
- docking of small molecules to proteins
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- rec: autogrid
- リガンドの受容体への結合を事前計算
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- rec: avogadro
- 分子可視化およびモデリングシステム
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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: bamtools
- BAM（ゲノムアラインメント）ファイルの操作用ツール
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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: bcbio
- toolkit for analysing high-throughput sequencing data
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- rec: bcftools
- ゲノムの variant call と VCF/BCF ファイルの操作
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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: 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
- 多重配列アライメントのプリティプリンティング
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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: bwa
- Burrows-Wheeler Aligner
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- rec: canu
- 一分子シークエンスゲノムアセンブラ
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- rec: cassiopee
- index and search tool in genomic sequences
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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: circlator
- ゲノムアセンブリの環状化
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- rec: circos
- データ可視化用プロット作成ツール
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- rec: clearcut
- extremely efficient phylogenetic tree reconstruction
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- rec: clonalframe
- 多座配列データを用いたバクテリアの小進化推定
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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: 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: 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: daligner
- ロングリードヌクレオチド配列間のローカルアラインメント発見
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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: deepnano
- MiniON ゲノム配列リード向け代替ベースコーラー
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- rec: delly
- Structural variant discovery by read analysis
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- rec: dialign
- Segment-based multiple sequence alignment
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- rec: dialign-tx
- セグメントベースの多重配列アライメント
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- rec: diamond-aligner
- accelerated BLAST compatible local sequence aligner
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- rec: dindel
- determines indel calls from short-read data
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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: dotter
- detailed comparison of two genomic sequences
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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
- ヨーロッパ分子生物学オープンソフトウェアスイート
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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: fastahack
- utility for indexing and sequence extraction from FASTA files
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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: 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: fastx-toolkit
- FASTQ/A short nucleotide reads pre-processing tools
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- rec: ffindex
- simple index/database for huge amounts of small files
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- rec: figtree
- グラフィカルな系統樹ビューア
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- rec: fitgcp
- fitting genome coverage distributions with mixture models
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- rec: flexbar
- flexible barcode and adapter removal for sequencing platforms
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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
- 汎用原子レベルモデリンググラフィックインターフェース (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
- 分子動力学シミュレーションの視覚化プログラム
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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: genometools
- versatile genome analysis toolkit
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- rec: gentle
- suite to plan genetic cloning
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- rec: gff2aplot
- pair-wise alignment-plots for genomic sequences in PostScript
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- rec: gff2ps
- GFF ファイルから PostScript 画像出力を作成
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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: giira
- RNA-Seq driven gene finding incorporating ambiguous reads
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- rec: glam2
- gapped protein motifs from unaligned sequences
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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
- 構築と解析ツールを含む分子動力学シミュレータ
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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
- タンパク質配列解析用のプロファイル隠れマルコフモデル
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- rec: hmmer2
- タンパク質配列解析用のプロファイル隠れマルコフモデル
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- rec: idba
- iterative De Bruijn Graph short read assemblers
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- rec: igor
- infers V(D)J recombination processes from sequencing data
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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: 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
- 反復ウイルス配列アセンブラー
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- rec: jaligner
- Smith-Waterman algorithm with Gotoh's improvement
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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
- 分子ビューア
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- rec: kalign
- グローバルおよびプログレッシブ多重配列アライメント
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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: kmc
- count kmers in genomic sequences
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- rec: kmer
- suite of tools for DNA sequence analysis
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- rec: kraken
- assigning taxonomic labels to short DNA sequences
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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: 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: 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: 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: logol
- Pattern matching tool using Logol language
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- rec: loki
- 一般的な家系の MCMC 連鎖分析
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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: 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: 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: mauve-aligner
- multiple genome alignment
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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: metaphlan2
- 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: 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
- PCR 派生データ保存用ツール
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- rec: mira-assembler
- Whole Genome Shotgun and EST Sequence Assembler
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- rec: mlv-smile
- Find statistically significant patterns in sequences
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- rec: mothur
- 微生物の研究のための配列解析スイート
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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: mummer
- 遺伝子全体の効率的な配列アライメント
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- rec: murasaki
- homology detection tool across multiple large genomes
- または murasaki-mpi
- homology detection tool across multiple large genomes (MPI-version)
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- rec: muscle
- タンパク質配列のマルチプルアライメントプログラム
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- rec: mustang
- multiple structural alignment of proteins
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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: nast-ier
- NAST-based DNA alignment tool
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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
- 生物学アプリケーション用 NCBI ライブラリ (Xベースユーティリティ)
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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: 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: 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: pal2nal
- converts proteins to genomic DNA alignment
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- rec: paleomix
- 古今の HTS データ処理用パイプラインおよびツール
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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: 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: pbalign
- map Pacific Biosciences reads to reference DNA sequences
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- rec: pbbarcode
- annotate PacBio sequencing reads with barcode information
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- rec: pbdagcon
- sequence consensus using directed acyclic graphs
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- rec: pbgenomicconsensus
- Pacific Biosciences variant and consensus caller
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- rec: pbh5tools
- tools for manipulating Pacific Biosciences HDF5 files
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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
- PCR 用プライマをグラフィカルに設計
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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: 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
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- rec: picard-tools
- Command line tools to manipulate SAM and BAM files
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- rec: piler
- genomic repeat analysis
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- rec: pilon
- automated genome assembly improvement and variant detection tool
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- rec: pirs
- Profile based Illumina pair-end Reads Simulator
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- rec: placnet
- Plasmid Constellation Network project
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- rec: plasmidomics
- プラスミドおよびベクタマップの描画と PostScript 画像出力
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- rec: plasmidseeker
- identification of known plasmids from whole-genome sequencing reads
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- rec: plast
- Parallel Local Sequence Alignment Search Tool
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- rec: plink
- whole-genome association analysis toolset
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- rec: plink1.9
- whole-genome association analysis toolset
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- rec: plip
- fully automated protein-ligand interaction profiler
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- rec: poa
- Partial Order Alignment for multiple sequence alignment
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- rec: populations
- population genetic software
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- rec: porechop
- adapter trimmer for Oxford Nanopore reads
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- rec: poretools
- toolkit for nanopore nucleotide sequencing data
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- rec: prank
- Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
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- rec: predictnls
- prediction and analysis of protein nuclear localization signals
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- rec: predictprotein
- suite of protein sequence analysis tools
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- rec: prime-phylo
- bayesian estimation of gene trees taking the species tree into account
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- rec: primer3
- tool to design flanking oligo nucleotides for DNA amplification
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- rec: proalign
- Probabilistic multiple alignment program
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- rec: probabel
- Toolset for Genome-Wide Association Analysis
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- rec: probalign
- multiple sequence alignment using partition function posterior probabilities
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- rec: probcons
- 確率的で整合性に基づく多重配列アライメント
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- rec: proda
- タンパク質配列のマルチプルアライメント
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- rec: prodigal
- Microbial (bacterial and archaeal) gene finding program
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- rec: profbval
- predictor of flexible/rigid protein residues from sequence
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- rec: profisis
- prediction of protein-protein interaction sites from sequence
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- rec: profnet-bval
- neural network architecture for profbval
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- rec: profnet-chop
- neural network architecture for profchop
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- rec: profnet-con
- neural network architecture for profcon
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- rec: profnet-isis
- neural network architecture for profisis
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- rec: profnet-md
- neural network architecture for metadisorder
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- rec: profnet-norsnet
- neural network architecture for norsnet
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- rec: profnet-prof
- neural network architecture for profacc
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- rec: profnet-snapfun
- neural network architecture for snapfun
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- rec: profphd
- secondary structure and solvent accessibility predictor
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- rec: profphd-net
- neural network architecture for profphd
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- rec: profphd-utils
- profphd helper utilities convert_seq and filter_hssp
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- rec: proftmb
- per-residue prediction of bacterial transmembrane beta barrels
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- rec: progressivemauve
- multiple genome alignment algorithms
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- rec: proteinortho
- Detection of (Co-)orthologs in large-scale protein analysis
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- rec: prottest
- selection of best-fit models of protein evolution
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- rec: pscan-chip
- ChIP-based identifcation of TF binding sites
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- rec: pscan-tfbs
- search for transcription factor binding sites
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- rec: psortb
- bacterial localization prediction tool
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- rec: pycorrfit
- tool for fitting correlation curves on a logarithmic plot
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- rec: pymol
- Molecular Graphics System
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- rec: pynast
- alignment of short DNA sequences
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- rec: pyscanfcs
- scientific tool for perpendicular line scanning FCS
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- rec: python-cogent
- framework for genomic biology
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- rec: python3-biomaj3-daemon
- BioMAJ daemon library
-
- rec: python3-gffutils
- Work with GFF and GTF files in a flexible database framework
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- rec: python3-presto
- toolkit for processing B and T cell sequences
-
- rec: python3-pybedtools
- Python 3 wrapper around BEDTools for bioinformatics work
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- rec: python3-pybel
- Biological Expression Language
-
- rec: python3-sqt
- SeQuencing Tools for biological DNA/RNA high-throughput data
-
- rec: pyvcf
- helper scripts for Variant Call Format (VCF) parser
-
- rec: qcumber
- quality control of genomic sequences
-
- rec: qtltools
- Tool set for molecular QTL discovery and analysis
-
- 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-bitseq
- transcript expression inference and analysis for RNA-seq data
-
- 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-dnacopy
- R package: DNA copy number data analysis
-
- rec: r-bioc-ebseq
- R package for RNA-Seq Differential Expression Analysis
-
- rec: r-bioc-genefilter
- methods for filtering genes from microarray experiments
-
- rec: r-bioc-geneplotter
- R package of functions for plotting genomic data
-
- rec: r-bioc-gviz
- Plotting data and annotation information along genomic coordinates
-
- rec: r-bioc-hilbertvis
- GNU R package to visualise long vector data
-
- rec: r-bioc-impute
- Imputation for microarray data
-
- rec: r-bioc-limma
- linear models for microarray data
-
- 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-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-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-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-shazam
- Immunoglobulin Somatic Hypermutation Analysis
-
- 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
- GNU R Statistical Exploration of Landscapes of Phylogenetic Trees
-
- rec: r-cran-vegan
- Community Ecology Package for R
-
- rec: r-other-hms-dbmi-spp
- 以下のパッケージによって提供される仮想パッケージです: r-cran-spp
-
- rec: r-other-mott-happy.hbrem
- GNU R package for fine-mapping complex diseases
-
- 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: 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: reapr
- universal tool for genome assembly evaluation
-
- rec: relion-bin
- toolkit for 3D reconstructions in cryo-electron microscopy
- または relion-bin+mpi
- parallel toolkit for 3D reconstructions in cryo-electron microscopy
-
- rec: relion-bin+gui
- parallel toolkit for 3D reconstructions in cryo-electron microscopy
- または relion-bin+mpi+gui
- parallel toolkit for 3D reconstructions in cryo-electron microscopy
-
- rec: repeatmasker-recon
- finds repeat families from biological sequences
-
- rec: reprof
- protein secondary structure and accessibility predictor
-
- 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: 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: salmon
- wicked-fast transcript quantification from RNA-seq data
-
- rec: samblaster
- marks duplicates, extracts discordant/split reads
-
- rec: samtools
- processing sequence alignments in SAM, BAM and CRAM formats
-
- rec: scoary
- pangenome-wide association studies
-
- 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: 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: sibsim4
- DNA テンプレート上で expressed RNA 配列を整列
-
- 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
- cDNA とゲノム DNA の整列用ツール
-
- rec: sim4db
- batch spliced alignment of cDNA sequences to a target genome
-
- rec: smalr
- interrogation of the methylation status of nucleotide sequencing reads
-
- rec: smalt
- Sequence Mapping and Alignment Tool
-
- rec: smithwaterman
- determine similar regions between two strings or genomic sequences
-
- 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: snpomatic
- fast, stringent short-read mapping software
-
- 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: 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: 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: 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: theseus
- superimpose macromolecules using maximum likelihood
-
- rec: tigr-glimmer
- 古細菌やバクテリアから遺伝子を発見
-
- rec: tm-align
- structural alignment of proteins
-
- rec: tnseq-transit
- 統計的な遺伝子もしくはゲノム領域の必須性計算
-
- rec: toil
- cross-platform workflow engine
-
- rec: tophat
- fast splice junction mapper for RNA-Seq reads
-
- rec: topp
- set of programs implementing The OpenMS Proteomic Pipeline
-
- rec: toppred
- transmembrane topology prediction
-
- 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
- 最尤法による系統樹の再構築
- または tree-ppuzzle
- 最尤法による系統樹の再構築 (並列化版)
-
- rec: treeview
- Java re-implementation of Michael Eisen's TreeView
-
- rec: treeviewx
- Displays and prints phylogenetic trees
-
- rec: trimmomatic
- flexible read trimming tool for Illumina NGS data
-
- rec: trinityrnaseq
- RNA-Seq De novo Assembly
-
- rec: tvc
- genetic variant caller for Ion Torrent sequencing platforms
-
- rec: uc-echo
- error correction algorithm designed for short-reads from NGS
-
- rec: unanimity
- generate and process accurate consensus nucleotide sequences
-
- rec: unicycler
- hybrid assembly pipeline for bacterial genomes
-
- rec: varna
- Visualization Applet for RNA
-
- rec: vcftools
- Collection of tools to work with VCF files
-
- rec: velvet
- 非常に短いリード用塩基配列アセンブラ
- または velvet-long
- Nucleic acid sequence assembler for very short reads, long version
-
- rec: velvetoptimiser
- automatically optimise Velvet do novo assembly parameters
-
- rec: viewmol
- graphical front end for computational chemistry programs
-
- rec: vsearch
- tool for processing metagenomic sequences
-
- rec: wigeon
- reimplementation of the Pintail 16S DNA anomaly detection utility
-
- rec: wise
- DNA 配列とタンパク質配列のような生体高分子の比較
-
- rec: yaha
- find split-read mappings on single-end queries
-
- rec: zalign
- parallel local alignment of biological sequences
-
- sug: acacia
- パッケージは利用できません
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- sug: adun.app
- Molecular Simulator for GNUstep (GUI)
-
- sug: amos-assembler
- パッケージは利用できません
-
- sug: amoscmp
- パッケージは利用できません
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- sug: annovar
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- sug: apollo
- パッケージは利用できません
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- sug: arachne
- パッケージは利用できません
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- sug: arb
- phylogenetic sequence analysis suite - main program
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- sug: asap
- パッケージは利用できません
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- sug: atropos
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- sug: autodocktools
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- sug: axparafit
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- sug: axpcoords
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- sug: bagpipe
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- sug: bambus
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- sug: bax2bam
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- sug: biceps
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- sug: big-blast
- パッケージは利用できません
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- sug: bigsdb
- パッケージは利用できません
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- sug: biobambam2
- パッケージは利用できません
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- sug: bismark
- パッケージは利用できません
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- sug: blat
- パッケージは利用できません
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- sug: blimps-utils
- blocks database improved searcher
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- sug: blobology
- パッケージは利用できません
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- sug: braker
- パッケージは利用できません
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- sug: btk-core
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- sug: cactus
- パッケージは利用できません
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- sug: caftools
- パッケージは利用できません
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- sug: cain
- simulations of chemical reactions
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- sug: card-rgi
- パッケージは利用できません
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- sug: ccs
- パッケージは利用できません
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- sug: cdna-db
- パッケージは利用できません
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- sug: cellprofiler
- パッケージは利用できません
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- sug: cinema
- パッケージは利用できません
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- sug: cluster3
- Reimplementation of the Eisen-clustering software
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- sug: cmap
- パッケージは利用できません
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- sug: compclust
- パッケージは利用できません
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- sug: condetri
- パッケージは利用できません
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- sug: contrafold
- パッケージは利用できません
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- sug: contralign
- パッケージは利用できません
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- sug: coot
- パッケージは利用できません
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- sug: copycat
- パッケージは利用できません
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- sug: crossbow
- パッケージは利用できません
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- sug: crux-toolkit
- パッケージは利用できません
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- sug: cufflinks
- Transcript assembly, differential expression and regulation for RNA-Seq
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- sug: cytoscape
- パッケージは利用できません
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- sug: dascrubber
- alignment-based scrubbing pipeline for DNA sequencing reads
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- sug: dazzle
- パッケージは利用できません
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- sug: deepbinner
- パッケージは利用できません
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- sug: dendroscope
- パッケージは利用できません
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- sug: e-hive
- パッケージは利用できません
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- sug: ecell
- パッケージは利用できません
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- sug: embassy-phylip
- EMBOSS conversions of the programs in the phylip package
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- sug: emboss-explorer
- web-based GUI to EMBOSS
-
- sug: emmax
- パッケージは利用できません
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- sug: emperor
- パッケージは利用できません
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- sug: ensembl
- パッケージは利用できません
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- sug: estferret
- パッケージは利用できません
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- sug: euler-sr
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- sug: euler2
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- sug: exabayes
- パッケージは利用できません
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- sug: exalt
- パッケージは利用できません
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- sug: excavator
- パッケージは利用できません
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- sug: falcon
- パッケージは利用できません
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- sug: fasta3
- tools for searching collections of biological sequences
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- sug: ffp
- パッケージは利用できません
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- sug: figaro
- パッケージは利用できません
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- sug: filtlong
- パッケージは利用できません
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- sug: forester
- パッケージは利用できません
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- sug: forge
- パッケージは利用できません
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- sug: galaxy
- パッケージは利用できません
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- sug: gassst
- パッケージは利用できません
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- sug: gatk
- パッケージは利用できません
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- sug: gbrowse-syn
- パッケージは利用できません
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- sug: genemark
- パッケージは利用できません
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- sug: genesplicer
- パッケージは利用できません
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- sug: genetrack
- パッケージは利用できません
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- sug: genezilla
- パッケージは利用できません
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- sug: genographer
- パッケージは利用できません
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- sug: getdata
- management of external databases
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- sug: gffread
- パッケージは利用できません
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- sug: glimmerhmm
- パッケージは利用できません
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- sug: gmap
- spliced and SNP-tolerant alignment for mRNA and short reads
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- sug: gmv
- パッケージは利用できません
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- sug: gramalign
- パッケージは利用できません
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- sug: haploview
- パッケージは利用できません
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- sug: hawkeye
- パッケージは利用できません
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- sug: htqc
- パッケージは利用できません
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- sug: igdiscover
- パッケージは利用できません
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- sug: igv
- パッケージは利用できません
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- sug: inspect
- パッケージは利用できません
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- sug: jalview
- パッケージは利用できません
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- sug: jbrowse
- パッケージは利用できません
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- sug: jigsaw
- パッケージは利用できません
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- sug: kallisto
- パッケージは利用できません
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- sug: kempbasu
- パッケージは利用できません
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- sug: kma
- パッケージは利用できません
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- sug: kmerresistance
- パッケージは利用できません
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- sug: kraken2
- パッケージは利用できません
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- sug: lofreq
- パッケージは利用できません
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- sug: mach-haplotyper
- パッケージは利用できません
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- sug: mage2tab
- パッケージは利用できません
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- sug: maker2
- パッケージは利用できません
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- sug: malt
- パッケージは利用できません
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- sug: manta
- パッケージは利用できません
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- sug: martj
- パッケージは利用できません
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- sug: maude
- high-performance logical framework
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- sug: maxd
- パッケージは利用できません
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- sug: meme
- パッケージは利用できません
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- sug: mesquite
- パッケージは利用できません
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- sug: metabit
- パッケージは利用できません
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- sug: metarep
- パッケージは利用できません
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- sug: metastudent-data
- predictor of Gene Ontology terms from protein sequence - data files
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- sug: metastudent-data-2
- predictor of Gene Ontology terms from protein sequence - data #2
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- sug: metastudent-data-3
- パッケージは利用できません
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- sug: mgltools-cadd
- Computer Aided Drug Discovery (CADD) Pipeline
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- sug: mgltools-pmv
- パッケージは利用できません
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- sug: mgltools-vision
- Python-based Visual Programming Environment
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- sug: migrate
- パッケージは利用できません
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- sug: minimus
- パッケージは利用できません
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- sug: mirbase
- パッケージは利用できません
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- sug: mirtop
- パッケージは利用できません
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- sug: mobyle
- Web portal that provides web forms for command-line software
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- sug: mobyle-programs
- program descriptions for the mobyle portal
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- sug: mobyle-tutorials
- program tutorials for the mobyle portal
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- sug: modeller
- パッケージは利用できません
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- sug: molekel
- パッケージは利用できません
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- sug: mosaik-aligner
- パッケージは利用できません
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- sug: mosdepth
- パッケージは利用できません
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- sug: mpsqed
- パッケージは利用できません
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- sug: mrs
- Information Retrieval System for Biomedical databanks
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- sug: msatfinder
- パッケージは利用できません
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- sug: msxpertsuite
- パッケージは利用できません
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- sug: mugsy
- パッケージは利用できません
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- sug: multiqc
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- sug: mummergpu
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- sug: mview
- パッケージは利用できません
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- sug: nanocall
- パッケージは利用できません
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- sug: ncbi-igblast
- パッケージは利用できません
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- sug: nextsv
- パッケージは利用できません
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- sug: ngila
- パッケージは利用できません
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- sug: ngsqctoolkit
- パッケージは利用できません
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- sug: nw-align
- パッケージは利用できません
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- sug: oases
- パッケージは利用できません
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- sug: obo-edit
- パッケージは利用できません
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- sug: oligoarrayaux
- パッケージは利用できません
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- sug: omegamap
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- sug: oncofuse
- パッケージは利用できません
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- sug: optimir
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- sug: paipline
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- sug: phpphylotree
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- sug: phylographer
- パッケージは利用できません
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- sug: phylophlan
- パッケージは利用できません
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- sug: phyloviz-core
- パッケージは利用できません
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- sug: phylowin
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- パッケージは利用できません
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- sug: plato
- パッケージは利用できません
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- sug: profit
- パッケージは利用できません
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- sug: prokka
- パッケージは利用できません
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- sug: prot4est
- パッケージは利用できません
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- sug: psipred
- パッケージは利用できません
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- sug: pssh2
- パッケージは利用できません
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- sug: pyrophosphate-tools
- パッケージは利用できません
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- sug: python-orange
- パッケージは利用できません
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- sug: python-reaper
- パッケージは利用できません
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- sug: python-treetime
- パッケージは利用できません
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- sug: python3-geneimpacts
- パッケージは利用できません
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- sug: qiime
- パッケージは利用できません
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- sug: qtlcart
- パッケージは利用できません
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- sug: qualimap
- パッケージは利用できません
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- sug: quast
- パッケージは利用できません
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- sug: r-bioc-annotationhub
- GNU R client to access AnnotationHub resources
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- sug: r-bioc-aroma.light
- BioConductor methods normalization and visualization of microarray data
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- sug: r-bioc-ensembldb
- GNU R utilities to create and use an Ensembl based annotation database
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- sug: r-bioc-go.db
- annotation maps describing the entire Gene Ontology
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- sug: r-bioc-savr
- GNU R parse and analyze Illumina SAV files
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- sug: r-cran-boolnet
- assembling, analyzing and visualizing Boolean networks
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- sug: r-cran-forecast
- パッケージは利用できません
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- sug: r-cran-pheatmap
- GNU R package to create pretty heatmaps
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- sug: r-cran-qqman
- R package for visualizing GWAS results using Q-Q and manhattan plots
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- sug: r-cran-rentrez
- GNU R interface to the NCBI's EUtils API
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- sug: r-cran-webgestaltr
- パッケージは利用できません
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- sug: r-other-apmswapp
- パッケージは利用できません
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- sug: raccoon
- パッケージは利用できません
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- sug: ragout
- パッケージは利用できません
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- sug: raxml-ng
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- sug: rbs-finder
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- sug: repeatmasker
- パッケージは利用できません
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- sug: rmblast
- パッケージは利用できません
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- sug: roadtrips
- パッケージは利用できません
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- sug: roche454ace2caf
- パッケージは利用できません
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- sug: rose
- パッケージは利用できません
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- sug: rsat
- パッケージは利用できません
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- sug: sailfish
- パッケージは利用できません
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- sug: sambamba
- パッケージは利用できません
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- sug: sap
- パッケージは利用できません
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- sug: science-workflow
- workflow management systems useful for scientific research
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- sug: seq-gen
- simulate the evolution of nucleotide or amino acid sequences
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- sug: seq-seq-pan
- パッケージは利用できません
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- sug: sequenceconverter.app
- パッケージは利用できません
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- sug: sibelia
- パッケージは利用できません
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- sug: sift
- predicts if a substitution in a protein has a phenotypic effect
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- sug: sina
- パッケージは利用できません
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- sug: sistr
- パッケージは利用できません
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- sug: situs
- パッケージは利用できません
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- sug: smrtanalysis
- パッケージは利用できません
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- sug: snpeff
- パッケージは利用できません
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- sug: solvate
- arranges water molecules around protein structures
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- sug: sourmash
- パッケージは利用できません
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- sug: spaln
- パッケージは利用できません
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- sug: sparta
- パッケージは利用できません
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- sug: splitstree
- パッケージは利用できません
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- sug: ssaha
- パッケージは利用できません
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- sug: strap
- パッケージは利用できません
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- sug: strap-base
- パッケージは利用できません
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- sug: stringtie
- パッケージは利用できません
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- sug: tab2mage
- パッケージは利用できません
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- sug: tacg
- パッケージは利用できません
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- sug: taverna
- パッケージは利用できません
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- sug: taxinspector
- パッケージは利用できません
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- sug: tetra
- パッケージは利用できません
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- sug: tide
- パッケージは利用できません
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- sug: tigr-glimmer-mg
- パッケージは利用できません
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- sug: tn-seqexplorer
- パッケージは利用できません
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- sug: treebuilder3d
- パッケージは利用できません
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- sug: treetime
- パッケージは利用できません
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- sug: tripal
- パッケージは利用できません
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- sug: trnascan-se
- detection of transfer RNA genes in genomic sequence
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- sug: twain
- パッケージは利用できません
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- sug: ugene
- パッケージは利用できません
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- sug: umap
- パッケージは利用できません
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- sug: umis
- パッケージは利用できません
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- sug: unc-fish
- パッケージは利用できません
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- sug: uniprime
- パッケージは利用できません
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- sug: varmatch
- パッケージは利用できません
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- sug: varscan
- variant detection in next-generation sequencing data
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- sug: vcfanno
- パッケージは利用できません
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- sug: vdjtools
- パッケージは利用できません
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- sug: vienna-rna
- パッケージは利用できません
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- sug: virulencefinder
- パッケージは利用できません
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- sug: vmd
- パッケージは利用できません
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- sug: x-tandem-pipeline
- パッケージは利用できません
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- sug: zodiac-zeden
- パッケージは利用できません