- [IQ-TREE] - [Java, v2.3.6, 2024.8] - [2020.02, Mol Biol Evol] - [IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.]
- [iqtree -m] - [Java, v2.3.6, 2024.8] - [2017.5, Nat Methods] - [ModelFinder: fast model selection for accurate phylogenetic estimates.]
- [fasttree2] - [C++, v2.1.11, NA] - [2010.03, PloS ONE] - [FastTree 2 -- Approximately Maximum-Likelihood Trees for Large Alignments.]
- [PhyloPhlAn] - [Python, v3.1.1, 2024.03] - [2020.05, Nat Commun] - [Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0.]
- [MrBayes] - [C] - [MRBAYES: Bayesian inference of phylogenetic trees.]
- [MrBayes] - [C, v3, ] - [2003.8, Bioinformatics] - [MrBayes 3: Bayesian phylogenetic inference under mixed models]
- [MrBayes] - [C, v3.2.7, 2020.1] - [2012.2, Syst Biol] - MRBAYES 3.2: Efficient Bayesian phylogenetic inference and model selection across a large model space.
- [trimAI] - [C++, v1.5.0, 2024.7] - [2009.8, Bioinformatics] - [trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.]
- [RAxML-NG] - [C++, v1.2.2, 2024.5] - [2019.11, Bioinformatics] - [RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.]
- [iTol] - [Web] - [2024.04, Nucleic Acids Res] - [Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool.]
- [ARB] - [需要转发, arb-7.0, 2021.09] [2004.03, Nucleic Acids Res] - [ARB: a software environment for sequence data.]
- [FigTree] - [Java, v1.4.5-pre, 2024.02]
- [GraPhlAn] - [Python, 1.1.3, 2020.06] - [2015.06, PeerJ] - [Compact graphical representation of phylogenetic data and metadata with GraPhlAn.]
- [phyTreeViz] - [Python, v0.2.0, 2024.1] - [Shimoyama, Y. (2023). phyTreeViz: Simple phylogenetic tree visualization python package [Computer software].]