[ 原始碼： debian-med ]
套件：med-cloud（3.8.1）
Debian Med bioinformatics applications usable in cloud computing
This metapackage will install Debian packages related to molecular biology, structural biology and bioinformatics for use in life sciences, that do not depend on graphical toolkits and therefore can fit on system images for use in cloud computing clusters, where space can be limited.
其他與 med-cloud 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: 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: 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: 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: 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: 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: bamtools
- toolkit for manipulating BAM (genome alignment) files
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- rec: bedtools
- suite of utilities for comparing genomic features
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- rec: bioperl
- Perl tools for computational molecular biology
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- rec: bioperl-run
- BioPerl wrappers: scripts
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- rec: biosquid
- utilities for biological sequence analysis
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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: bwa
- Burrows-Wheeler Aligner
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- rec: cassiopee
- index and search tool in genomic 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: 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: 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: 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: datamash
- statistics tool for command-line interface
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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: 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: dssp
- protein secondary structure assignment based on 3D structure
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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: exonerate
- generic tool for pairwise sequence comparison
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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: fastqc
- quality control for high throughput sequence data
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- rec: fasttree
- phylogenetic trees from alignments of nucleotide or protein sequences
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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: freecontact
- fast protein contact predictor
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- rec: gasic
- genome abundance similarity correction
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- rec: genometools
- versatile genome analysis toolkit
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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: 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: 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: hhsuite
- sensitive protein sequence searching based on HMM-HMM alignment
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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: idba
- iterative De Bruijn Graph short read assemblers
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- rec: infernal
- inference of RNA secondary structural alignments
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- rec: jellyfish
- count k-mers in DNA sequences
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- rec: kalign
- Global and progressive multiple sequence alignment
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- rec: kissplice
- Detection of various kinds of polymorphisms in RNA-seq data
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- rec: last-align
- genome-scale comparison of biological sequences
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- rec: loki
- MCMC linkage analysis on general pedigrees
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- rec: macs
- Model-based Analysis of ChIP-Seq on short reads sequencers
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- rec: mafft
- Multiple alignment program for amino acid or nucleotide 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: melting
- compute the melting temperature of nucleic acid duplex
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- rec: minia
- short-read biological sequence assembler
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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: mlv-smile
- Find statistically significant patterns in sequences
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- rec: mothur
- sequence analysis suite for research on microbiota
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- rec: mrbayes
- Bayesian Inference of Phylogeny
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- rec: mummer
- Efficient sequence alignment of full genomes
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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: ncbi-epcr
- Tool to test a DNA sequence for the presence of sequence tagged sites
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- rec: ncbi-tools-bin
- NCBI libraries for biology applications (text-based utilities)
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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: 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: pdb2pqr
- Preparation of protein structures for electrostatics calculations
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- rec: perm
- efficient mapping of short reads with periodic spaced seeds
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- rec: phyml
- Phylogenetic estimation using Maximum Likelihood
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- rec: phyutility
- simple analyses or modifications on both phylogenetic trees and data matrices
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- rec: picard-tools
- Command line tools to manipulate SAM and BAM files
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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: plink2
- whole-genome association analysis toolset
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- rec: poa
- Partial Order Alignment for multiple sequence alignment
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- rec: prank
- Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
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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: probabel
- Toolset for Genome-Wide Association Analysis
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- rec: probcons
- PROBabilistic CONSistency-based multiple sequence alignment
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- rec: proda
- multiple alignment of protein sequences
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- rec: prodigal
- Microbial (bacterial and archaeal) gene finding program
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- rec: python3-biomaj3-cli
- BioMAJ client
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- rec: python3-biopython
- Python3 library for bioinformatics
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- rec: python3-cogent3
- framework for genomic biology
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- rec: qiime
- Quantitative Insights Into Microbial Ecology
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- rec: r-bioc-edger
- Empirical analysis of digital gene expression data in R
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- rec: r-bioc-hilbertvis
- GNU R package to visualise long vector data
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- rec: r-cran-pvclust
- Hierarchical Clustering with P-Values via Multiscale Bootstrap
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- rec: r-cran-qtl
- GNU R package for genetic marker linkage analysis
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- rec: r-cran-vegan
- Community Ecology Package for R
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- rec: r-other-mott-happy.hbrem
- GNU R package for fine-mapping complex diseases
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- rec: raster3d
- tools for generating images of proteins or other molecules
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- rec: readseq
- Conversion between sequence formats
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- rec: rnahybrid
- Fast and effective prediction of microRNA/target duplexes
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- rec: rtax
- Classification of sequence reads of 16S ribosomal RNA gene
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- rec: samtools
- processing sequence alignments in SAM, BAM and CRAM formats
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- rec: seqan-apps
- C++ library for the analysis of biological sequences
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- rec: sibsim4
- align expressed RNA sequences on a DNA template
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- rec: sigma-align
- Simple greedy multiple alignment of non-coding DNA sequences
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- rec: sim4
- tool for aligning cDNA and genomic DNA
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- rec: smalt
- Sequence Mapping and Alignment Tool
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- rec: snap
- location of genes from DNA sequence with hidden markov model
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- rec: soapdenovo
- short-read assembly method to build de novo draft assembly
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- rec: soapdenovo2
- short-read assembly method to build de novo draft assembly
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- rec: squizz
- Converter for genetic sequences and alignments
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- rec: sra-toolkit
- utilities for the NCBI Sequence Read Archive
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- rec: ssake
- genomics application for assembling millions of very short DNA sequences
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- rec: staden-io-lib-utils
- programs for manipulating DNA sequencing files
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- rec: t-coffee
- Multiple Sequence Alignment
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- rec: tabix
- generic indexer for TAB-delimited genome position files
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- rec: theseus
- superimpose macromolecules using maximum likelihood
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- rec: tigr-glimmer
- Gene detection in archea and bacteria
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- rec: tree-puzzle
- Reconstruction of phylogenetic trees by maximum likelihood
- 或者 tree-ppuzzle
- Parallelized reconstruction of phylogenetic trees by maximum likelihood
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- rec: vcftools
- Collection of tools to work with VCF files
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- rec: velvet
- Nucleic acid sequence assembler for very short reads
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- rec: wise
- comparison of biopolymers, like DNA and protein sequences
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- sug: anfo
- 套件暫時不可用
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- sug: bagpipe
- 套件暫時不可用
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- sug: blast2
- 套件暫時不可用
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- sug: cufflinks
- Transcript assembly, differential expression and regulation for RNA-Seq
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- sug: embassy-phylip
- 套件暫時不可用
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- sug: giira
- 套件暫時不可用