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[ Source: physamp  ]

Package: physamp (1.1.0-5)

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sample sequence alignment corresponding to phylogeny

The PhySamp package currently contains two programs: bppphysamp, which samples sequences according to their similarity, and bppalnoptim, which samples a sequence alignment by removing sequences in order to maximize the number of sites suitable for a given analysis. The bppalnoptim program has three running modes:

 * Interactive: the user will be iteratively proposed a set of choices
   for sequence removal, with their corresponding site gains. The
   procedure stops when the user does not want to remove more sequences,
   and the resulting filtered alignment is written.
 * Automatic: the user enters an a priori criterion for stopping
   the filtering procedure (for instance a minimum number of
   sequences to keep).
 * Diagnostic: this mode allows one to plot the trade-off curve, by
   showing the site gain as a function of the number of removed
   sequences.

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Download physamp

Download for all available architectures
Architecture Package Size Installed Size Files
alpha (unofficial port) 181.2 kB1,893.0 kB [list of files]
amd64 182.3 kB1,774.0 kB [list of files]
arm64 175.9 kB1,826.0 kB [list of files]
armel 169.6 kB1,724.0 kB [list of files]
armhf 170.5 kB1,660.0 kB [list of files]
hppa (unofficial port) 186.0 kB1,807.0 kB [list of files]
i386 185.3 kB1,768.0 kB [list of files]
ia64 (unofficial port) 193.3 kB1,996.0 kB [list of files]
m68k (unofficial port) 178.1 kB1,752.0 kB [list of files]
mips64el 177.9 kB1,912.0 kB [list of files]
ppc64 (unofficial port) 187.3 kB1,954.0 kB [list of files]
ppc64el 186.1 kB1,890.0 kB [list of files]
riscv64 182.1 kB1,714.0 kB [list of files]
s390x 181.0 kB1,790.0 kB [list of files]
sh4 (unofficial port) 188.5 kB1,826.0 kB [list of files]
sparc64 (unofficial port) 170.3 kB3,497.0 kB [list of files]
x32 (unofficial port) 180.4 kB1,740.0 kB [list of files]