added upper bound on kappa, renumbering in addHybrid

src/phyLiNCoptimization.jl

@@ -8,6 +8,7 @@ const likAbsDelHybLiNC = -0.1 #= loglik decrease allowed when removing a hybrid
   lower (more negative) values of lead to more hybrids removed during the search =#
 const alphaRASmin = 0.02
 const alphaRASmax = 50.0
+const kappamax = 10.0
 
 """
     CacheGammaLiNC
@@ -713,7 +714,7 @@ function addhybridedgeLiNC!(obj::SSM, currLik::Float64, maxhybrid::Int,
     newhybridnode, newhybridedge = result
     # unzip only at new node and its child edge
     unzipat_canonical!(newhybridnode, getChildEdge(newhybridnode))
-    updateSSM!(obj)
+    updateSSM!(obj, true; constraints=constraints)
     optimizelocalgammas_LiNC!(obj, newhybridedge, ftolRel, γcache)
     if newhybridedge.gamma == 0.0
         deletehybridedge!(obj.net, newhybridedge, false,true) # nofuse,unroot

src/traitsLikDiscrete.jl

@@ -511,6 +511,9 @@ function fit!(obj::SSM; optimizeQ=true::Bool, optimizeRVAS=true::Bool,
         NLopt.maxeval!(optQ, maxeval) # max number of iterations
         # NLopt.maxtime!(optQ, t::Real)
         NLopt.lower_bounds!(optQ, zeros(Float64, nparQ))
+        if typeof(obj.model) == HKY85 # set an upper bound on kappa values
+            NLopt.upper_bounds!(optQ, fill(kappamax,nparQ))
+        end
         # fixit: set upper bound depending on branch lengths in network?
         NLopt.max_objective!(optQ, loglikfun)
         fmax, xmax, ret = NLopt.optimize(optQ, obj.model.rate)