RAxML-NG v1.1.0

This release introduces several features/bugfixes that improve speed and/or accuracy of constrained tree search, especially in case of an incomplete constraint tree.

Constrained tree search improvements

• switch to a new constraint check approach based on split compatibility (old method still available via --extra constraint-old)
• allow user and parsimony-based starting trees in combination with topological constraint
• use 10 random + 10 parsimony starting trees by default (previously: 20 random)
• --check/--parse will check compatibility with constraint if specified (eg raxml-ng --check --msa aln.fa --model GTR+G --tree-constraint cons.nw --tree tree2check.nw)

Other

• add --bs-write-msa flag to write out bootstrap MSAs from main inference run (PR #125, thanks to @harmsm)
• fix assertion when rooting a multifurcating tree (#130)