bali-phy
Bayesian Inference of Alignment and Phylogeny
Command lineScience
Not tested on a device yet. What that means
Commands in the package
bali-phyalignment-catalignment-chop-internalalignment-consensusalignment-distancesalignment-drawalignment-findalignment-gildalignment-indicesalignment-infoalignment-maxalignment-thinalignment-translatealignments-diffbali-phy-pkgbali-subsamplebp-analyzecut-rangedraw-treeextract-ancestorsmcon-toolmctree-mean-lengthsmodel_Ppickoutstatreportstats-selectsummarize-ancestorstree-mean-lengthstree-tooltrees-bootstraptrees-consensustrees-distancestrees-to-SRQ
About bali-phy
From Debian's package description
BAli-Phy estimates multiple sequence alignments and evolutionary trees from unaligned DNA, amino acid, or codon sequences. BAli-Phy uses MCMC to estimate evolutionary trees, positive selection, and branch lengths while averaging over alternative alignments. BAli-Phy can display alignment ambiguity graphically in an alignment uncertainty (AU) plot.
BAli-Phy can also estimate phylogenies from a fixed alignment (like MrBayes and BEAST) using substitution models like GTR+gamma. BAli-Phy automatically estimates relative rates for each gene.
From Debian's description of the bali-phy package, under that package's license.
Dependencies
Depends on
libboost-chrono1.83.0t64libboost-json1.83.0libboost-program-options1.83.0libboost-random1.83.0libc6libcairo2libfmt10libgcc-s1libstdc++6perlpython3
Recommends
r-basegnuplot
Related apps
- snaplocation of genes from DNA sequence with hidden markov modelCommand line
- gdal-binGeospatial Data Abstraction Library - Utility programsCommand line
- fsaFast Statistical Alignment of protein, RNA or DNA sequencesCommand line
- ncbi-blast+next generation suite of BLAST sequence search toolsCommand line
- gbrowseGMOD Generic Genome BrowserCommand line
- ea-utilscommand-line tools for processing biological sequencing dataCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the bali-phy package, under that package's license.
- Description: Debian's description of the bali-phy package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.