added code to incorporate Guyanagaster data
fixed error in Abyss command

Abyss requires the output name to be supplied as an ABSOLUTE path rather than a
relative one because it ends up making some nonsense sym links otherwise. I just added
a cd command so that I don't have to supply a path at all
added scripts to run RAxML in parallel on a cluster

I haven't figured out how to automate this entirely, but these scripts can be used to
analyse all of the alignments once they've been uploaded to the cluster using the
following command: bash SumbitAll.bash

(Alignments must be in ~/Alignments, RunRaxml.bash must be in ~/shell, and there must be a
folder called ~/Trees)

I still need to specify the outgroup (with -o Con_pu1,Ser_laS73,Ser_laS79 or some subset thereof)

Alignments need to be converted to phylip and names have to be paired down to just the species name
fixed rule for Copci ref genes

The touch command was updating the wrong Copci folder, causing these commands to rerun
every time.
fixed typo in Cli_neb command