Changed the location of java to /software/bin/java. Added search location of pecan.jar file to look in /software/ensembl/compara/pecan/. Changed default_jar_file to pecan_v0.8.jar. Removed -X flag from pecan arguments. Changed location of EstimateTree.py to /software/ensembl/compara/pecan/.
Changed the location of java to /software/bin/java. Added search location of pecan.jar file to look in /software/ensembl/compara/pecan/. Changed default_jar_file to pecan_v0.8.jar. Removed -X flag from pecan arguments. Changed location of EstimateTree.py to /software/ensembl/compara/pecan/.

kiwiroy/ensembl-analysis,Ensembl/ensembl-analysis,james-monkeyshines/ensembl-analysis,mn1/ensembl-analysis,Ensembl/ensembl-analysis,mn1/ensembl-analysis,kiwiroy/ensembl-analysis,Ensembl/ensembl-analysis,james-monkeyshines/ensembl-analysis,mn1/ensembl-analysis,james-monkeyshines/ensembl-analysis