[Biojava-dev] Problem regarding ScoreType

[Ian Agius]

Hi all,
I'm new to BioJava and was checking out what the ScoreType
Probability,Null_MODEL and ODDS do exactly. I was trying to access the API
but some of the pages were down for a reason. Do you know how I can access
them? Also do you know whats the difference betweens the mentioned
scoretypes?

Im building some Profile HMMs of a set of protein sequences. I want to
compare an unknown sequence to a number of profiles that I have created, and
then choose the most probable profile to determine the family type. Ive
tried using both ODDS and PROBABILITY but I am unsure which one to use when.
Also I had some negative probabilities (-0.26) when using PROBABILITY and
various results when using odds (from 300.12 to 25.6).

One of the links that was down:
http://www.biojava.org/docs/api/org/biojava/bio/dp/ScoreType.Odds.html

Happy new year to all

regards Ian