prime-phylo

bayesian estimation of gene trees taking the species tree into account

Command lineScience

Not tested on a device yet. What that means

Commands in the package

chainsaw
mcmc_analysis
primeDLRS
primeDTLSR
primeGEM
primeGSRf
reconcile
reroot
showtree
tree2leafnames
treesize

About prime-phylo

From Debian's package description

PrIME (Probabilistic Integrated Models of Evolution) is a package supporting inference of evolutionary parameters in a Bayesian framework using Markov chain Monte Carlo simulation. A distinguishing feature of PrIME is that the species tree is taken into account when analyzing gene trees.
The input data to PrIME is a multiple sequence alignment in FASTA format and the output data contains trees in Newick format.

From Debian's description of the prime-phylo package, under that package's license.

Dependencies

Depends on

perl
libblas3orlibblas.so.3
libboost-mpi1.83.0
libboost-serialization1.83.0
libc6
libgcc-s1
liblapack3orliblapack.so.3
libopenmpi40
libstdc++6
libxml2

Related apps

lokiMCMC linkage analysis on general pedigreesCommand line
gbrowseGMOD Generic Genome BrowserCommand line
GwyddionSPM data visualization and analysis
jagsJust Another Gibbs Sampler for Bayesian MCMC - binaryCommand line
gretlEconometrics package
phymlPhylogenetic estimation using Maximum LikelihoodCommand line

All Linux science apps

Sources and licenses

Name: the Debian package name.
Summary: Debian's short description of the prime-phylo package, under that package's license.
Description: Debian's description of the prime-phylo package, under that package's license.
Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
Popularity: Debian Popularity Contest counts.