Write trees for DNDS analysis to correct dir
Write trees for DNDS analysis to correct dir

(also changes the names of files to fix up, phyML does not append .txt
to these files, at least in v3.3.2 on linux)

nextgenusfs/funannotate,nextgenusfs/funannotate,nextgenusfs/funannotate,nextgenusfs/funannotate