bppphysamp

sample sequence alignment corresponding to phylogeny

Install

All systems
curl cmd.cat/bppphysamp.sh
Debian Debian
apt-get install physamp
Ubuntu
apt-get install physamp
image/svg+xml Kali Linux
apt-get install physamp
Windows (WSL2)
sudo apt-get update sudo apt-get install physamp
Raspbian
apt-get install bppsuite
Dockerfile
dockerfile.run/bppphysamp

physamp

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.

bppsuite

Bio++ program suite

The Bio++ Program Suite is a package of programs using the Bio++ libraries and dedicated to Phylogenetics and Molecular Evolution. All programs are independent, but can be combined to perform rather complex analyses. These programs use the interface helper tools of the libraries, and hence share the same syntax. They also have several options in common, which may also be shared by third-party software. The following programs are included: - BppML for maximum likelihood analysis, - BppSeqGen for sequences simulation, - BppAncestor for ancestral states reconstruction, - BppDist for distance methods, - BppPars for parsimony analysis, - BppSeqMan for file conversion and sequence manipulation, - BppConsense for building consensus tree and computing bootstrap values, - BppReRoot for tree rerooting. - BppTreeDraw for tree drawing. - BppAlnScore for comparing alignments and computing alignment scores. - BppMixedLikelihoods for computing site per site likelihoods of components of mixture models. - BppPopGen for population genetics analyses.