Historical and contingent features affect re-evolution of a complex trait lost during mass extinction
(Journal of Evolutionary Biology 2008)
SOURCE CODE DISTRIBUTION
Avida_v2.1_distrib.tar--distribution of Avida source code used to run main experiments
ENVIRONMENT FILES
env.9cd3_lossy--environment file used for main experiments
env.9cd3_lossyEMPTY--environment file used for replay experiments
resourcetest.dat--file of resource levels to be loaded for determining per-site information content
EVENT FILES
evnt9rCD3dropAB_5KPR1KRST_FULL.cfg--event file used to get full population after 1000 updates of post-extinction recovery for clade traces
evnt9rCD3dropAB_5KPR5KRST_FULL.cfg --event file used to get full population after 2000 and 5000 updates of post-extinction recovery for clade traces
evnt9rCD3dropAB_nopress_100KU_ECOSTBL.cfg --event file used for main experiments, to get pre-extinction full and ecologically stable communities
evnt9rCD3dropAB_nopress_205KU_ECOSTBL.cfg--event file used for main experiments, to get control population after 205000 updates in absence of press episode (full and ecologically stable population)
evnt9rCD3dropAB_RESTE_205KU_ECOSTBL.cfg--event file used for main experiments, with extinction and recovery (full and ecologically stable populations)
evnt9rCD3_injseqindivrec100K.cfg --event file used for replay experiments (organism sequences in file REPLAY_SEQUENCES.xls)
ANALYZE MODE FILES
EXAMPLE_ANALYZE_SCRIPTS --file containing example analyze mode scripts for lineage traces, clade traces, sequence alignments, and data needed for genotype-phenotype maps and execution trace plots
EXPERIMENT STARTUP FILES
genesis--main file with master startup parameter settings (world description, mutation rates etc.)
organism.heads.50--default seed ancestor used to start all main experiments
ADDITIONAL DATA
REPLAY_SEQUENCES.xls --Excel file containing sequences of organisms used for replay experiments (used with evnt9rCD3_injseqindivrec100K.cfg)