start og revamp by getting command line working again...
1st draft of dynamic outgroup.  zero testing yet
get dynamic outgroup running
fix more bugs in dynamic outgroup.  time for unit tests
sort ougroups list output by coverage.  fix branch computations
Merge remote-tracking branch 'origin/development' into ogselection
hack in candidateset support for dynamic outgroup tho really shouldnt be necessary
clean dynamicoutgroup interface a bit to be more consistent with existing codes and add some basic unit tests
add error about unfinished high degree code.  let outgroup.py run even if no graphviz
make grpahviz output more consistent for commandline
add logic to get input sequence paths directly out of project xml
replace bioio fasta read with specialized version
oops
add interface for dynamic outgroup
oops
oops
oops
add --root option to cactus_createMultiCactusProject.py to help with root outgroups.. still need to figure out issues with preprocessor
Fix mismatch in # of sequences between expTemplate & project xml
use cactus_analyseAssembly to for fasta stats and only do dynamic programming at given root.  still need to incorporate n50 into opt fun