Fixed 0^0 issue; removed bumping up lower bound in Bracket; added some verbose debugging infrastrure
Demote ConjugateGradient error to a warning
Adding check for cURL in CMake
Merge pull request #167 from stevenweaver/master

Adding check for cURL in CMake
CURL patch
adding additional curl checks
Merge pull request #168 from stevenweaver/master

Defining __HYPHYCURL__ in CMake as opposed to in the codebase.
Added a fix to seq aligners where there would be gaps relative to the reference on the 3' end
Merge branch 'master' of github.com:veg/hyphy
Added missing GUI includes into bayesgraph.cpp
Fixed always setting SEQ_ALIGN_NO_TP to 0 in SeqAlignCodonShared
Map --- to - in defineCodonToAA
Linux GCC does not search include paths recursively, explicitly adding the sqlite path to include path
Changing recommended from Dual to Proportional
Merge branch 'master' of github.com:veg/hyphy
Merge branch 'master' of github.com:stevenweaver/hyphy
Merge pull request #171 from stevenweaver/master

GCC does not search include paths recursively, explicitly adding t...
Added support for a regularizing LF_SMOOTHING_SCALER
Added support for a regularizing LF_SMOOTHING_SCALER
Merge branch 'master' of github.com:veg/hyphy