{"refrec":{"BRefID":363557,"RR":"<b>Xiang, C.-Y.; Gao, F.; Jakovlic, I.; Lei, H.-P.; Hu, Y.; Zhang, H.; Zou, H.; Wang, G.-T.; Zhang, D.</b> (2023). Using PhyloSuite for molecular phylogeny and tree‐based analyses. <i>iMeta 2(1)</i>: e87. <a href=\"https://dx.doi.org/10.1002/imt2.87\" target=\"_blank\">https://dx.doi.org/10.1002/imt2.87</a>","BEntID":361275,"PublicFlag":1,"CheckedFlag":0,"wosflag":0,"vabbflag":0,"RefStringPartII":". <i>iMeta 2(1)</i>: e87. <a href=\"https://dx.doi.org/10.1002/imt2.87\" target=\"_blank\">https://dx.doi.org/10.1002/imt2.87</a>","DocTypID":8,"DocType":"Journal article","MarineFlag":0,"FreshFlag":0,"BrackishFlag":0,"TerrestrialFlag":0,"Authorstring":"Xiang, C.-Y.; Gao, F.; Jakovlic, I.; Lei, H.-P.; Hu, Y.; Zhang, H.; Zou, H.; Wang, G.-T.; Zhang, D.","OrigTitleTranslFlag":0,"Authorstringtrunc":"Xiang, C.-Y. <i>et al.</i>","Englishabstract":"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.","AbstractOtherLang":null,"BibLvlCode":"AS","StandardTitle":"Using PhyloSuite for molecular phylogeny and tree‐based analyses","OrigTitleLangCode":"en","OrigTitleLangCodeExtended":"eng","OrigTitleLangID":15,"DateLastModified":{"date":"2024-12-10 01:33:17.368041","timezone_type":1,"timezone":"+01:00"},"UserAccessRight":null,"UserAccID":null,"AuthorKeywords":null,"OtherDescriptors":null,"Notes":null,"AnaPub":2023,"MonPub":null,"DateUpdate":"2023-04-11","DateCreate":"2023-04-11","SecASFANote":null,"ConfID":null,"PeerRev":1,"VlizCoreFlag":1,"WoScode":"WOS:001136693100007","VABBcode":null,"OpenAcc":0,"DOI":"10.1002/imt2.87"},"refs":null,"anarec":{"AnaID":363557,"PubliDate":2023,"Pagination":"e87","XtraPublOfAnaID":null,"ISBN":null,"Volume":"2","Issue":"1","BRefMon":null,"BRefMonRR":null,"BRefXtra":null,"BRefXtraRR":null,"SerBRefID":363556,"SerRR":"iMeta. 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