Package: gubbins (3.3.3-1 and others)

[ Source: gubbins  ]

phylogenetic analysis of genome sequences

Gubbins supports rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.

Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.

Other Packages Related to gubbins

• dep: fasttree [not amd64, i386]

  phylogenetic trees from alignments of nucleotide or protein sequences

• dep: libc6 (>= 2.27) [riscv64]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

  dep: libc6 (>= 2.29) [m68k, ppc64]

  dep: libc6 (>= 2.34) [amd64, i386]

• dep: libc6.1 (>= 2.29) [alpha]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6.1-udeb

• dep: python3

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

• dep: python3-biopython

  Python3 library for bioinformatics

• dep: python3-dendropy

  DendroPy Phylogenetic Computing Library (Python 3)

• dep: python3-multiprocess [amd64, i386]

  better multiprocessing and multithreading in Python

• dep: python3-nose [not amd64, i386]

  test discovery and running for Python3 unittest

• dep: python3-numpy [amd64, i386]

  Fast array facility to the Python language (Python 3)

• dep: python3-reportlab [not amd64, i386]

  ReportLab library to create PDF documents using Python3

• dep: python3-scipy [amd64, i386]

  scientific tools for Python 3

• dep: raxml

  Randomized Axelerated Maximum Likelihood of phylogenetic trees

• dep: zlib1g (>= 1:1.1.4)

  compression library - runtime

• rec: fasttree

  phylogenetic trees from alignments of nucleotide or protein sequences

• rec: iqtree

  efficient phylogenetic software by maximum likelihood

• rec: python3-numba

  native machine code compiler for Python 3

• sug: r-base-core

  GNU R core of statistical computation and graphics system

Download gubbins

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	2.3.5-1	53.5 kB	201.0 kB	[list of files]
amd64	3.3.3-1	89.4 kB	474.0 kB	[list of files]
i386	3.3.3-1	90.5 kB	477.0 kB	[list of files]
m68k (unofficial port)	2.3.5-1	46.0 kB	174.0 kB	[list of files]
ppc64 (unofficial port)	2.3.5-1	55.4 kB	312.0 kB	[list of files]
riscv64 (unofficial port)	2.3.5-1	48.1 kB	168.0 kB	[list of files]