InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet burial.alphabet ReadAlphabet burial-sep.alphabet ReadAlphabet two-spot-burial.alphabet InFilePrefix CreatePredBurialCost pred_nb11_2k near-backbone-11 T0378.t2k.near-backbone-11.rdb near_backbone CreatePredBurialCost pred_nb11_2k_simple near-backbone-11 T0378.t2k.near-backbone-11.rdb near_backbone simple CreatePredBurialCost pred_nb11_04 near-backbone-11 T0378.t04.near-backbone-11.rdb near_backbone CreatePredBurialCost pred_nb11_04_simple near-backbone-11 T0378.t04.near-backbone-11.rdb near_backbone simple CreatePredBurialCost pred_nb11_06 near-backbone-11 T0378.t06.near-backbone-11.rdb near_backbone CreatePredBurialCost pred_nb11_06_simple near-backbone-11 T0378.t06.near-backbone-11.rdb near_backbone simple CreatePredAlphaCost pred_alpha2k alpha11 T0378.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0378.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0378.t06.alpha.rdb 2 alpha alpha_prev sum InFilePrefix /projects/compbio/experiments/undertaker/spots/ CreateBurialCost cb14 CB smoothed-monomeric-50pc-CB14.hist CB InFilePrefix CreatePredBurialCost pred_cb14_2k CB_burial_14_7 T0378.t2k.CB_burial_14_7.rdb cb14 CreatePredBurialCost pred_cb14_2k_simple CB_burial_14_7 T0378.t2k.CB_burial_14_7.rdb cb14 simple CreatePredBurialCost pred_cb14_04 CB_burial_14_7 T0378.t04.CB_burial_14_7.rdb cb14 CreatePredBurialCost pred_cb14_04_simple CB_burial_14_7 T0378.t04.CB_burial_14_7.rdb cb14 simple CreatePredBurialCost pred_cb14_06 CB_burial_14_7 T0378.t06.CB_burial_14_7.rdb cb14 CreatePredBurialCost pred_cb14_06_simple CB_burial_14_7 T0378.t06.CB_burial_14_7.rdb cb14 simple InFilePrefix /projects/compbio/experiments/undertaker/spots/ CreateBurialCost CB8-sep9 CB dunbrack-40pc-3157-CB8-sep9.hist spot min_sep 9 InFilePrefix CreatePredBurialCost pred_CB8-sep9_06 CB8-sep9 T0378.t06.CB8-sep9.rdb CB8-sep9 CreatePredBurialCost pred_CB8-sep9_06_simple CB8-sep9 T0378.t06.CB8-sep9.rdb CB8-sep9 simple SetCost near_backbone 5 \ pred_nb11_2k_simple 5 \ pred_nb11_2k 5 \ pred_nb11_04_simple 5 \ pred_nb11_04 5 \ pred_nb11_06_simple 5 \ pred_nb11_06 5 \ cb14 5 \ pred_cb14_2k_simple 5 \ pred_cb14_2k 5 \ pred_cb14_04_simple 5 \ pred_cb14_04 5 \ pred_cb14_06_simple 5 \ pred_cb14_06 5 \ pred_alpha2k 3 \ pred_alpha04 4 \ pred_alpha06 5 \ CB8-sep9 5 pred_CB8-sep9_06 5 pred_CB8-sep9_06_simple 5