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[ Source: clonalframeml  ]

Package: clonalframeml (1.12-2)

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Efficient Inference of Recombination in Whole Bacterial Genomes

ClonalFrameML is a software package that performs efficient inference of recombination in bacterial genomes. ClonalFrameML was created by Xavier Didelot and Daniel Wilson. ClonalFrameML can be applied to any type of aligned sequence data, but is especially aimed at analysis of whole genome sequences. It is able to compare hundreds of whole genomes in a matter of hours on a standard Desktop computer. There are three main outputs from a run of ClonalFrameML: a phylogeny with branch lengths corrected to account for recombination, an estimation of the key parameters of the recombination process, and a genomic map of where recombination took place for each branch of the phylogeny.

ClonalFrameML is a maximum likelihood implementation of the Bayesian software ClonalFrame which was previously described by Didelot and Falush (2007). The recombination model underpinning ClonalFrameML is exactly the same as for ClonalFrame, but this new implementation is a lot faster, is able to deal with much larger genomic dataset, and does not suffer from MCMC convergence issues

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Architecture Package Size Installed Size Files
alpha (unofficial port) 100.5 kB314.0 kB [list of files]
amd64 103.8 kB281.0 kB [list of files]
arm64 86.3 kB233.0 kB [list of files]
armel 87.6 kB248.0 kB [list of files]
armhf 84.3 kB176.0 kB [list of files]
hppa (unofficial port) 99.4 kB258.0 kB [list of files]
i386 102.7 kB288.0 kB [list of files]
ia64 (unofficial port) 131.1 kB576.0 kB [list of files]
m68k (unofficial port) 93.0 kB264.0 kB [list of files]
mips64el 91.9 kB287.0 kB [list of files]
mipsel 94.3 kB293.0 kB [list of files]
ppc64 (unofficial port) 96.8 kB337.0 kB [list of files]
ppc64el 100.7 kB337.0 kB [list of files]
riscv64 (unofficial port) 94.7 kB205.0 kB [list of files]
s390x 88.8 kB269.0 kB [list of files]
sh4 (unofficial port) 121.6 kB252.0 kB [list of files]
sparc64 (unofficial port) 87.1 kB260.0 kB [list of files]
x32 (unofficial port) 106.8 kB280.0 kB [list of files]