Many tools are there for phylogenetic analysis- AncesTree, AliGROOVE, ape, Armadillo Workflow Platform, BAli-Phy, BATWING, BayesPhylogenies, BayesTraits, BEAST, BioNumerics , Bosque BUCKy, Canopy , CITUP, ClustalW, Dendroscope, EzEditor , fastDNAml , FastTree 2, fitmodel , Geneious , HyPhy, IQPNNI, IQ-TREE , jModelTest 2, LisBeth , MEGA, MegAlign Pro, Mesquite, MetaPIGA2 , Modelgenerator, MOLPHY, MorphoBank, MrBayes, Network, Nona , PAML, ParaPhylo, PartitionFinder, PASTIS, PAUP, phangorn, Phybase, phyclust , PHYLIP , phyloT ,PhyloQuart, PhyloWGS , PhyML ,phyx , POY, ProtTest 3, PyCogent, QuickTree, RAxML-HPC , RAxML-NG, SEMPHY, sowhat , SplitsTree, TNT , TOPALi , TreeGen , TreeAlign, Treefinder, TREE-PUZZLE, T-REX (Webserver), UGENE, Winclada, Xrate etc.
Which one do you prefer most?
I think Nextclade is user-friendly. And this tool needs some development, especially in the tree building process.
Kouadri Mohamed El Amine
Dear Researcher,
Thanks for your response. Are these tools open source-based online tools?
Kouadri Mohamed El Amine. If you are looking for a tool for phylogenetic analysis, then your decision should be based on a number of factors such as the algorithm(eg maximum likelihood) , datasize, sequence type (nucleotide or amino acid),etc. You can read the manual for the tools to make a decision.
If you are looking to perform some preliminary analysis, then you can watch these tutorials
RAxML: https://youtu.be/NBiBuec2C_8
PhyML: https://youtu.be/9SniaKyUGfk
Thanks, Vincent Appiah
By the way, have any suggestions on which phylogenetic tool has the most perfect visualization performance?
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