Building the BioNJ trees

[KYQiu21]

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.

[stephaneguindon]

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

[KYQiu21]

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!

[stephaneguindon]

Did you use the '-d aa' option?

[KYQiu21]

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

[stephaneguindon]

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