FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix. FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle 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 open-source software -- you can download the code below. 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), WAG (Whelan & Goldman 2001), or LG (Le and Gascuel 2008) models 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”).
Keywords for this software
References in zbMATH (referenced in 9 articles )
Showing results 1 to 9 of 9.
- Richards, Andrew; Kubatko, Laura: Bayesian-weighted triplet and quartet methods for species tree inference (2021)
- Willson, James; Roddur, Mrinmoy Saha; Warnow, Tandy: Comparing methods for species tree estimation with gene duplication and loss (2021)
- Andres Veidenberg, Ari L: Pline: automatic generation of modern web interfaces for command-line programs (2020) arXiv
- Warnow, Tandy (ed.): Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret (2019)
- Russell Y. Neches; Camille Scott: SuchTree: Fast, thread-safe computations with phylogenetic trees (2018) not zbMATH
- Brown, Daniel G.; Truszkowski, Jakub: Fast error-tolerant quartet phylogeny algorithms (2013)
- Moret, Bernard M. E.; Lin, Yu; Tang, Jijun: Rearrangements in phylogenetic inference: compare, model, or encode? (2013)
- Warnow, Tandy: Large-scale multiple sequence alignment and phylogeny estimation (2013)
- Brown, Daniel G.; Truszkowski, Jakub: Fast error-tolerant quartet phylogeny algorithms (2011)