README

Example use of LGA:

perl driverInitial.pl -seq=example/sample.fa -alignment=example/sample.phy -new=example/sample.first.new -score=example/sample.score -tnt=tnt_global_search.pl -fs=sample
perl driverIterations.pl -seq=example/sample.fa -alignment=example/sample.phy -gt=example/sample.first.new -new=example/sample.new -score=example/sample.score -tnt=tnt_global_search.pl -b4jump=2 -dist2jump=2 -fs=sample

For more information about these parameters, type "perl driverInitial.pl -help" and "perl driverIterations.pl -help".

Depending on the arguments passed to the LGA scripts, the following programs may be required to execute:
Clustalw can be downloaded at ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/.
Dnapars can be downloaded at http://evolution.genetics.washington.edu/phylip/getme.html.
Ruby can be downloaded at http://www.ruby-lang.org/.
Muscle can be downloaded at http://www.drive5.com/muscle/.
Recidcm3 can be downloaded at http://www.cs.njit.edu/~usman/RecIDCM3.html.
SODA can be downloaded at http://csl.cs.byu.edu/soda/ (forthcoming).
PAUP can be purchased at http://paup.csit.fsu.edu/.
TNT can be purchased by following instructions detailed at http://www.cladistics.org/downloads/webtnt.html.