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[ Source: clonalframe  ]

Package: clonalframe (1.2-9)

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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

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Architecture Package Size Installed Size Files
alpha (unofficial port) 51.7 kB148.0 kB [list of files]
amd64 48.6 kB127.0 kB [list of files]
arm64 44.0 kB115.0 kB [list of files]
armel 41.9 kB110.0 kB [list of files]
armhf 40.7 kB82.0 kB [list of files]
hppa (unofficial port) 53.1 kB137.0 kB [list of files]
hurd-i386 52.5 kB126.0 kB [list of files]
i386 52.5 kB126.0 kB [list of files]
kfreebsd-amd64 48.5 kB123.0 kB [list of files]
kfreebsd-i386 52.5 kB126.0 kB [list of files]
m68k (unofficial port) 46.7 kB122.0 kB [list of files]
mips 51.4 kB145.0 kB [list of files]
mips64el 53.0 kB159.0 kB [list of files]
mipsel 52.0 kB145.0 kB [list of files]
powerpcspe (unofficial port) 49.5 kB146.0 kB [list of files]
ppc64 (unofficial port) 52.5 kB211.0 kB [list of files]
ppc64el 52.5 kB147.0 kB [list of files]
riscv64 (unofficial port) 48.3 kB104.0 kB [list of files]
s390x 46.1 kB131.0 kB [list of files]
sh4 (unofficial port) 53.0 kB115.0 kB [list of files]
sparc64 (unofficial port) 43.4 kB126.0 kB [list of files]
x32 (unofficial port) 48.0 kB118.0 kB [list of files]