[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].]
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