Addresses Issue #87.  Create test code for PIC format ASR confidence value input to predict_traits.py
Addresses issue #87.  Adds script interface option to specify ASR confidence file format: confidence_interval (default) or sigma
Addresses Issue #87 Adds code for calculating the brownian motion parameter from confidence intervals (as returned by PIC)
Addresses Issue #87 Partial fix for compatibility with PIC based CI intervals.
Working commit.  Fixes format issues and allows prediction of brownian motion parameters from PIC CIs.  Thus we can run predict traits normally using the inferred rate parameters.  However, an additional round of commits is needed to use information from nodes with multiple sequenced children in setting the brownian motion parameter.
Added support for multiple brownian motion parameters, one per gene.   Additional testing needed.
Added support for multiple brownian motion parameters.  Work in progress.
Added test code for inferring brownian motion parameters from PIC confidence intervals
Addresses Issue #87.  Adds additional test code for processing variances/brownian motion parameters as arrays with one value per trait rather than single values
Addresses Issue #87.  Changes several functions to accomodate arrays of per-trait variance.
Minor commit before rebase
minor commit prior to rebase
Updated test to allow for confidence interval output from predict traits
Addresses Issue #87. Addresses Issue #104.  Modifies predict_traits_from_ancestors to output confidence intervals, removes option to exclude known tips from predictions, uses known tips in prediction
Final commit before pull request.
Added output of upper and lower confidence interval files for predictions.
Final commit before pull request.  Validated that known genomes are now no longer predicted.
Merge branch 'master' of github.com:picrust/picrust