added list of output files
added code to run RAxML to make file

this required changing the locations of input and output files

I need to figure out how to automate running this remotely
added code to run augustus on VirtualBox thru ssh
added code to remove sequences consisting of only gaps
modified to skip alignment with zero characters
added a hack to exclude gene 6661, which is all screwed up
changed location of score summary files
added code to create a partitions file
changed location of input and output files

The locations do not match their location on the local computer, but I am going to add
code to copy them to these locations on the remote server and to run the jobs there
changed the name of the assembly file to end in -scaffolds.fa
changed path to augustus executable so original location so other config files are visible
changed the name of outfiles so they don't clash with the non-partitioned analysis
added location of shell scripts on cluster
added code to copy alignments to cluster and run RAxML