Update Phyml.pm

[qifei9]

I updated Phyml.pm to:

• Fix issues Bio::Tools::Run::Phylo::Phyml use default parameter for interleaved input, but it use sequential input #43 and Bio::Tools::Run::Phylo::Phyml, rand_starts cannot be set to 0 #44. The previous commit aiming these two issues did not actually fix them;
• Make it compatible to -b (--bootstrap) option which could be set to 0, -1, -2, -4, -5;
• Make parameters with value 0 could be passed to functions.