Пакет: augur (11.0.0-1)

[ Источник: 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

Другие пакеты, относящиеся к augur

• dep: fasttree

  phylogenetic trees from alignments of nucleotide or protein sequences

• dep: iqtree

  efficient phylogenetic software by maximum likelihood

• dep: mafft

  Multiple alignment program for amino acid or nucleotide sequences

• dep: python3

  интерактивный высокоуровневый объектно-ориентированный язык (версия python3 по умолчанию)

• dep: python3-bcbio-gff

  Python3 library to read and write Generic Feature Format

• dep: python3-biopython

  Python3 library for bioinformatics

• dep: python3-boto (>= 2.38.0)

  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-jsonschema

  An(other) implementation of JSON Schema (Draft 3 and 4) - Python 3.x

• dep: python3-matplotlib (>= 1.5.1)

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

• dep: python3-packaging

  core utilities for python3 packages

• dep: python3-pandas (>= 0.16.2)

  data structures for "relational" or "labeled" data

• dep: python3-schedule

  Job scheduling for humans (Python 3)

• dep: python3-seaborn (>= 0.6.0)

  statistical visualization library for Python3

• dep: python3-treetime

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

• dep: raxml

  синтез филогенетических деревьев по методу максимального правдоподобия

• dep: seqmagick

  imagemagick-like frontend to Biopython SeqIO

• dep: vcftools

  Collection of tools to work with VCF files

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