I am attemping to use phylonet to investigate the gene flow among species. My input are gene trees with branch length and bootstraps. I have tried three formats of the same input trees but got different output network, without any error report. So could someone tell me which format is the correct one for phylonet? Thanks ! The three formats I used as below:
- ((SpeA : BL, Spe: BL)BL : BS , SpeC : BL); ### BL : branch length; BS : bootstrap
- ((SpeA : BL, Spe: BL) : BL : BS , SpeC : BL); ### add a ":" after the ")"
- ((SpeA : BL, Spe: BL) : BL , SpeC : BL); ### remove the bootstrap
only format 2 got the "#H1" in the output network.