((/taspi/tree-score/ambig-score.lisp::reassign-ambig-help (nil nil nil nil (if) nil nil) ((nil) nil (consp) nil (if) nil nil) ((actual-seq) nil nil (equal cons cons) nil nil nil) (nil nil (car quote cdr) nil (if recursive-call recursive-call) nil nil) ((actual-seq N cssl-map cssl-map) nil (not car cdar cdr cdr cdr cdr) (assoc-hqual) nil nil nil) ((pars-seq-scorelist cssl-map actual-seq pars-seq-scorelist cssl-map actual-seq pars-seq-scorelist) nil (car) (equal) nil nil nil) ((actual-seq) nil (car cdr) nil nil nil nil)) (/taspi/tree-score/ambig-score.lisp::get-key-matching-val (nil nil nil nil (if) nil nil) ((nil) nil (consp) nil (if) nil nil) ((mapping) nil (caar) (equal recursive-call) nil nil nil) ((val mapping val) nil (cdar cdr) nil nil nil nil) ((mapping mapping) nil nil nil nil nil nil) (nil nil nil nil nil nil nil) (nil nil nil nil nil nil nil)) (/taspi/tree-score/ambig-score.lisp::reassign-ambig2 (nil nil nil nil (if) nil nil) ((nil) nil (consp) (let*) nil nil nil) ((pars-seqs-scorelist) nil nil ((poss-internal-name (get-key-matching-val (caar pars-seqs-scorelist) anc-mappings))) (if) nil nil) ((Error in reassign-ambig2) nil (internal-name one-actual-seq) (equal cons) nil nil nil) (nil nil (cdr len len) (cons) (if) (recursive-call) nil) ((poss-internal-name poss-internal-name one-actual-seq actual-seq cssl-map anc-mappings) nil (caar cdar caar cdr) (assoc-hqual) (reassign-ambig-help) nil nil) ((pars-seqs-scorelist internal-name actual-seq pars-seqs-scorelist pars-seqs-scorelist one-actual-seq cssl-map pars-seqs-scorelist) nil (cdar) nil nil nil nil)) (/taspi/tree-score/ambig-score.lisp::make-sequence-pairings-for-tree-from-scorelists-and-actual (nil nil nil nil (mv-let) nil nil) (nil nil (total) nil (if) (score-tree-and-sequences-keep-internal) nil) ((pairings tree sequence-score-lists matrix-lists nil Error: Bad pairings from score-tree-and-keep-internal) nil (alistp-gen) (let) nil nil nil) ((pairings (reassigned-pairings (reassign-ambig2 (cons (cons tree total) pairings) sequences cssl-map anc-mapping))) nil nil nil (if) nil nil) ((Error: Need good pairings from reassign-ambig) nil (alistp-gen make-sequence-pairings) nil nil nil nil) ((reassigned-pairings reassigned-pairings) nil nil nil nil nil nil) (nil nil nil nil nil nil nil)) (/taspi/tree-score/ambig-score.lisp::score-tree-with-affine-score-lists-ambig (nil nil nil nil (if) nil nil) (nil nil (consp) (let) nil nil nil) ((anc-mappings (pairings (make-sequence-pairings-for-tree-from-scorelists-and-actual tree score-lists sequences (get-matrix-lists-from-trans transition-matrix) cssl-map anc-mappings)) tree score-lists gap-char gap-cost gap-extend-cost transition-matrix anc-mappings) nil nil nil (if) nil nil) ((pairings) nil (consp) nil nil (score-pairings) nil) ((pairings pairings) (0) (quote) nil nil (list) nil) ((affine gap-char gap-cost gap-extend-cost) nil nil (numberfy) nil nil nil) ((transition-matrix) (0) nil nil nil nil nil)))