Paketti: augur (20.0.0-1)

[ Source: augur  ]

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

Muut pakettiin augur liittyvät paketit

• dep: fasttree

  phylogenetic trees from alignments of nucleotide or protein sequences

• dep: mafft

  Multiple alignment program for amino acid or nucleotide sequences

• dep: python3

  interactive high-level object-oriented language (default python3 version)

• dep: python3-bcbio-gff

  Python3 library to read and write Generic Feature Format

• dep: python3-biopython

  Python3 library for bioinformatics

• dep: python3-boto3

  Python interface to Amazon's Web Services - Python 3.x

• dep: python3-cvxopt

  Python3 package for convex optimization

• dep: python3-dendropy

  DendroPy Phylogenetic Computing Library (Python 3)

• dep: python3-ipdb

  IPython-based pdb replacement (Python 3 version)

• dep: python3-isodate

  ISO 8601 date/time/duration parser and formatter (Python 3 module)

• dep: python3-jsonschema

  An(other) implementation of JSON Schema (Draft 3, 4, 6, 7)

• dep: python3-matplotlib

  Python based plotting system in a style similar to Matlab (Python 3)

• dep: python3-networkx

  tool to create, manipulate and study complex networks (Python3)

• dep: python3-numpy

  Fast array facility to the Python 3 language

• dep: python3-packaging

  core utilities for python3 packages

• dep: python3-pandas

  data structures for "relational" or "labeled" data

• dep: python3-pyfastx

  fast random access to sequences from FASTA/Q file - python3 module

• dep: python3-schedule

  Job scheduling for humans (Python 3)

• dep: python3-scipy

  scientific tools for Python 3

• dep: python3-seaborn

  statistical visualization library for Python3

• dep: python3-treetime (>= 0.9.4)

  inference of time stamped phylogenies and ancestral reconstruction (Python 3)

• dep: python3-xopen (>= 1.7.0-1~)

  Python3 module to open compressed files transparently

• dep: python3-zstandard

  Python bindings for interfacing with Zstandard library

• dep: raxml

  Randomized Axelerated Maximum Likelihood of phylogenetic trees

• dep: seqmagick

  imagemagick-like frontend to Biopython SeqIO

• dep: vcftools

  Collection of tools to work with VCF files

• rec: iqtree

  efficient phylogenetic software by maximum likelihood

Imuroi augur

Imurointi kaikille saataville arkkitehtuureille

Arkkitehtuuri	Paketin koko	Koko asennettuna	Tiedostot
all	182.9 kt	829.0 kt	[tiedostoluettelo]