fasttree
phylogenetic trees from alignments of nucleotide or protein sequences
Command lineScience
Not tested on a device yet. What that means
Commands in the package
FastTreefasttreefasttreeMP
About fasttree
From Debian's package description
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It handles alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7.
FastTree is more accurate than PhyML 3 with default settings, and much more accurate than the distance-matrix methods that are traditionally used for large alignments. FastTree uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT (Jones-Taylor-Thornton 1992) model of amino acid evolution. To account for the varying rates of evolution across sites, FastTree uses a single rate for each site (the "CAT" approximation). To quickly estimate the reliability of each split in the tree, FastTree computes local support values with the Shimodaira-Hasegawa test (these are the same as PhyML 3's "SH-like local supports").
This package contains a single threaded version (fasttree) and a parallel version which uses OpenMP (fasttreMP).
From Debian's description of the fasttree package, under that package's license.
Dependencies
Depends on
libc6libgomp1
Related apps
- samtoolsprocessing sequence alignments in SAM, BAM and CRAM formatsCommand line
- hmmerprofile hidden Markov models for protein sequence analysisCommand line
- muscleMultiple alignment program of protein sequencesCommand line
- clustaloGeneral-purpose multiple sequence alignment program for proteinsCommand line
- mafftMultiple alignment program for amino acid or nucleotide sequencesCommand line
- ncbi-entrez-directNCBI Entrez utilities on the command lineCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the fasttree package, under that package's license.
- Description: Debian's description of the fasttree 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.