Basic questions about PTP and mPTP

Lorena Corina Bezerra de Lima

unread,

Oct 15, 2016, 10:23:00 AM10/15/16

to PTP species delimitation

Hello everyone!

I have some questions about PTP and mPTP (a bit basic, sorry for it ...):

1) Please, could someone explain to me, more clearly what it is: acceptance rate, merge, split, mean and Bayesian support value, on the PTP server? (I saw similar questions in the google group, but I still don't understand ... sorry)

2) Can I use input trees generated by any method, such as parsimony, likelihood or Bayesian inference?

3) mPTP is available in command line only for linux?

Thank you all!

Paschalia Kapli

unread,

Oct 17, 2016, 8:24:21 AM10/17/16

to Lorena Corina Bezerra de Lima, PTP species delimitation

Dear Lorena,

please find the answers to your questions below

Hello everyone!

I have some questions about PTP and mPTP (a bit basic, sorry for it ...):

1) Please, could someone explain to me, more clearly what it is: acceptance rate, merge, split, mean and Bayesian support value, on the PTP server? (I saw similar questions in the google group, but I still don't understand ... sorry)

regarding the bayesian inference of PTP you could check here: http://sco.h-its.org/exelixis/pubs/dissZhang.pdf . For details of the MCMC sampling of mPTP please take a look at the manuscript http://biorxiv.org/content/biorxiv/early/2016/07/14/063875.full.pdf and paragraph 3 in the supplementary material, you can also find a description of the support values for mPTP in the github wiki (https://github.com/Pas-Kapli/mptp/wiki/Species-delimitation-using-Markov-Chain-Monte-Carlo#support-values-and-credible-intervals)

2) Can I use input trees generated by any method, such as parsimony, likelihood or Bayesian inference?

You can use any phylogenetic tree as long as the branch lengths represent substitutions per site, so Maximum Likelihood and Bayesian Inference trees are ok but not Parsimony trees.

3) mPTP is available in command line only for linux?

Using the instructions from the github wiki (https://github.com/Pas-Kapli/mptp) you should be able to compile it in Mac too. In the next couple of days we will release a pre-comiled binary for Windows as-well! In the meantime, if you are using windows you can also use the online server http://mptp.h-its.org/.

Best regards,

Paschalia

Lorena Corina Bezerra de Lima

unread,

Oct 17, 2016, 8:27:05 AM10/17/16

to Paschalia Kapli, PTP species delimitation

Thank you!

--

Lorena Corina Bezerra de Lima
Laboratório de Ecologia e Evolução
Instituto Butantan
Av. Dr. Vital Brazil, 1500
São Paulo, SP - Brasil - 05503-900
Tel.: +55 (11) 2627 9812

Reply all

Reply to author

Forward