[ 原始碼： augur ]
套件：augur（24.4.0-1）
pipeline components for real-time virus analysis
The nextstrain project is an attempt to make flexible informatic pipelines and visualization tools to track ongoing pathogen evolution as sequence data emerges. The nextstrain project derives from nextflu, which was specific to influenza evolution.
nextstrain is comprised of three components:
* fauna: database and IO scripts for sequence and serological data * augur: informatic pipelines to conduct inferences from raw data * auspice: web app to visualize resulting inferences
其他與 augur 有關的套件
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- dep: fasttree
- phylogenetic trees from alignments of nucleotide or protein sequences
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- dep: mafft
- Multiple alignment program for amino acid or nucleotide sequences
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- dep: python3
- interactive high-level object-oriented language (default python3 version)
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- dep: python3-bcbio-gff
- Python3 library to read and write Generic Feature Format
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- dep: python3-biopython
- Python3 library for bioinformatics
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- dep: python3-boto3
- Python interface to Amazon's Web Services - Python 3.x
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- dep: python3-cvxopt
- Python3 package for convex optimization
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- dep: python3-dendropy
- DendroPy Phylogenetic Computing Library (Python 3)
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- dep: python3-importlib-resources
- Read resources from Python packages
- 或者 python3-supported-min (>= 3.11)
- 套件暫時不可用
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- dep: python3-ipdb
- IPython-based pdb replacement (Python 3 version)
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- dep: python3-isodate
- ISO 8601 date/time/duration parser and formatter (Python 3 module)
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- dep: python3-jsonschema
- An(other) implementation of JSON Schema
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- dep: python3-matplotlib
- Python based plotting system in a style similar to Matlab
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- dep: python3-networkx
- tool to create, manipulate and study complex networks (Python3)
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- dep: python3-numpy
- Fast array facility to the Python language (Python 3)
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- dep: python3-packaging
- core utilities for python3 packages
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- dep: python3-pandas
- data structures for "relational" or "labeled" data
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- dep: python3-pyfastx
- fast random access to sequences from FASTA/Q file - python3 module
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- dep: python3-schedule
- Job scheduling for humans (Python 3)
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- dep: python3-scipy
- scientific tools for Python 3
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- dep: python3-seaborn
- statistical visualization library for Python3
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- dep: python3-treetime (>= 0.9.4)
- inference of time stamped phylogenies and ancestral reconstruction (Python 3)
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- dep: python3-xopen (>= 1.7.0-1~)
- Python3 module to open compressed files transparently
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- dep: python3-zstandard
- Python bindings for interfacing with Zstandard library
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- dep: raxml
- Randomized Axelerated Maximum Likelihood of phylogenetic trees
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- dep: seqmagick
- imagemagick-like frontend to Biopython SeqIO
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- dep: vcftools
- Collection of tools to work with VCF files
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- rec: iqtree
- efficient phylogenetic software by maximum likelihood