Package: clonalframe (1.2-10 and others)

[ Source: clonalframe  ]

inference of bacterial microevolution using multilocus sequence data

ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.

ClonalFrame can be applied to any kind of sequence data, from a single fragment of DNA to whole genomes. It is well suited for the analysis of MLST data, where 7 gene fragments have been sequenced, but becomes progressively more powerful as the sequenced regions increase in length and number up to whole genomes. However, it requires the sequences to be aligned. If you have genomic data that is not aligned, it is recommend to use Mauve which produces alignment of whole bacterial genomes in exactly the format required for analysis with ClonalFrame.

Tags: Implemented in: C++, Role: Program

Other Packages Related to clonalframe

• dep: libc6 (>= 2.14) [amd64]

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

  dep: libc6 (>= 2.17) [arm64, ppc64el]

  dep: libc6 (>= 2.7) [not amd64, arm64, ppc64el]

• dep: libgcc-s1 (>= 3.0) [not armel, armhf]

  GCC support library

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

• dep: libgsl25 (>= 2.6)

  GNU Scientific Library (GSL) -- library package

• dep: libstdc++6 (>= 5.2)

  GNU Standard C++ Library v3

• sug: clonalframeml

  Efficient Inference of Recombination in Whole Bacterial Genomes

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amd64	1.2-10+b1	49.4 kB	136.0 kB	[list of files]
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armel	1.2-10+b1	42.7 kB	115.0 kB	[list of files]
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s390x	1.2-10+b1	47.0 kB	136.0 kB	[list of files]