Hey guys
Why would species tree of the same species constructed with different software programmes be different. I constructed a species using PhyloT with NCBI taxon IDs ( short cut to demonstrate phylogenetic relationship between fungal species) but the topology of the tree is different from other species trees reported in literature for the same species generated with different methods and programs. Like the phylogenetic relationship between the species deviates from what is reported in other papers or MyCocosm.
In general terms, each software may produce different outcomes, based on the input data, the algorithms used, and parameters. For this specific example, it should be noted that the tree you get from PhyloT, despite the name, is not a phylogenetic tree, but a taxonomic tree. Of course, taxonomic classification and groups should respect the latest results from phylogenetic analyses. Phylogenetic trees are mostly based on molecular data, sequence information and conservation, and eventually, the fossil record, while taxonomy uses as "input data" the combined knowledge of taxonomists, with the "algorithm": reaching some sort of "social consensus", if you will. Also, taxonomic trees have constant branch lengths because they are concerned with the dependencies between names of things. Phylogenetic trees, on the other hand, are meant for depicting evolutionary events.
