Using PhyloSuite for molecular phylogeny and tree‐based analyses
Xiang, C.-Y.; Gao, F.; Jakovlic, I.; Lei, H.-P.; Hu, Y.; Zhang, H.; Zou, H.; Wang, G.-T.; Zhang, D. (2023). Using PhyloSuite for molecular phylogeny and tree‐based analyses. iMeta 2(1): e87. https://dx.doi.org/10.1002/imt2.87
In: iMeta. Wiley: Australia. ISSN 2770-5986; e-ISSN 2770-596X, more
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| Authors | | Top |
- Xiang, C.-Y.
- Gao, F.
- Jakovlic, I.
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- Lei, H.-P.
- Hu, Y.
- Zhang, H.
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- Zou, H.
- Wang, G.-T.
- Zhang, D.
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| Abstract |
Phylogenetic analysis has entered the genomics (multilocus) era. For less experienced researchers, conquering the large number of software programs required for a multilocus-based phylogenetic reconstruction can be somewhat daunting and time-consuming. PhyloSuite, a software with a user-friendly GUI, was designed to make this process more accessible by integrating multiple software programs needed for multilocus and single-gene phylogenies and further streamlining the whole process. In this protocol, we aim to explain how to conduct each step of the phylogenetic pipeline and tree-based analyses in PhyloSuite. We also present a new version of PhyloSuite (v1.2.3), wherein we fixed some bugs, made some optimizations, and introduced some new functions, including a number of tree-based analyses, such as signal-to-noise calculation, saturation analysis, spurious species identification, and etc. The step-by-step protocol includes background information (i.e., what the step does), reasons (i.e., why do the step), and operations (i.e., how to do it). This protocol will help researchers quick-start their way through the multilocus phylogenetic analysis, especially those interested in conducting organelle-based analyses. |
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