Dear Yabier,

you should calculate the strict consensus tree of your most parimonious trees. On this tree you should assign the bootstrap support values (branches that were not found in the bootstrap analysis have support

Dear Yabier,

you should calculate the strict consensus tree of your most parimonious trees. On this tree you should assign the bootstrap support values (branches that were not found in the bootstrap analysis have support

Thank you, Martin.

In the end I tried to make some quality trees I've seen in Fungal Diversity papers and some other journals, that include the topology from a most parsimonious tree, thickened branches for those that are present in the strict consensus tree, bootstrap values from MP and extra support values from an alternative method (in my case, ML with GARLI).

I wrote a small tutorial in a forum in case somebody may want to do something similar. You can check it here:

http://www.protocol-online.org/forums/topic/30587-parsimony-trees-using-paup/?p=161962

Some ideas are discussed in https://www.researchgate.net/publication/235601668_Incorporating_molecular_data_in_fungal_systematics_a_guide_for_aspiringresearchers?ev=prf_pub

Article Incorporating molecular data in fungal systematics: A guide ...

Xabier Vázquez Campos I got the same problem with you, so I followed the step that you put in your link. But I get stuck in this step "Now, reload the Ratchet trees generated, to ease the labour make a nexus file (I call it gettreesbest.nex) like this:". So, what do you meant by reload the Ratchet tree? or I need to create another nexus file (like you call gettreesbest.nex). Thank you very much in advance for your answer.

Hard to say, I wrote that 5 years ago and I haven't use PAUP* again.

As far as I remember you need to create a nexus file as the one described and loading in into PAUP* so you load only the best trees from the ratchet iteration search.

Otherwise you need to run the gettrees command manually 20 time if you made 20 ratchet iterations.