phyml Building the BioNJ trees

Building the BioNJ trees

Open KYQiu21 opened this issue 1 year ago • 5 comments

Dear all,

Is it possible to infer only the BioNJ trees given a sequence alignment? If so, what is the parameter setting for this? Thanks.

Best, K.

Mar 24 '23 15:03 KYQiu21

./phyml -i your_sequences -o none should do the trick

Mar 24 '23 16:03 stephaneguindon

Thanks for your reply! I tested this with the proteic file in the example folder, it returns bugs:

. 429 patterns found (out of a total of 547 sites). . 136 sites without polymorphism (24.86%). Illegal instruction

How should I address this? Many thanks!

Mar 27 '23 14:03 KYQiu21

Did you use the '-d aa' option?

Mar 28 '23 14:03 stephaneguindon

Yes! ./phyml -i example_dataset -o none -d aa gives the error report I posted above

Mar 28 '23 14:03 KYQiu21

Could you please indicate which version of PhyML you're running, which OS and how you compiled?

Mar 28 '23 14:03 stephaneguindon