Confidence interval output for predict_traits.py and use of known genomes

This pull request addresses Issue #86 and fixes Issue #104.

Changes:

Issue #86

-- predict_traits.py can now output confidence interval and variance files.  Currently if users ask for confidence intervals one table of variances, one 95% upper CI table, and one 95% lower CI table are created.  

--All variance methods now work with ace_pic output.  Brownian motion parameters are inferred from the supplied confidence intervals.

-- Variance functions updated to work with arrays of values, so as to accomodate multiple variances (one per gene).

-- Added test code for these steps.

Issue #104

-- Removed the option to not use known tips in predictions (this was a relic from an older benchmarking scheme: we don't need it).

-- Ensured that known values are used instead of predictions.