how can I do estimation of nucleotide biases using HyPhy or Datamonkey?

The fastest way I can think of is to use one of the automated nucleotide model selection tools on Datamonkey.
- a.

To expand on that:
- upload your alignment to Datamonkey
- at the Analysis Setup menu, press the "Execute" button at the bottom of the page to run an automatic model selection tool
- Datamonkey will fit all possible reversible models to your data, and select one candidate based on performance with respect to AIC (Akaike's Information Criterion)
- to interpret the model string (a sequence of 6 integers), reading from left to right, each integer assigns a substitution type (lexicographical order) to a rate class; for example, 010010 means that (AC, AT, CG, and GT) belong to one class and that (AG, GT) belong to a second.

- a.

thanks that really helped.....