physamp

sample sequence alignment corresponding to phylogeny

Description

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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Homepage

https://jydu.github.io/physamp/

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