8@  @ __text__TEXT! @C__data__DATA!$Pj __cstring__TEXT"%__literal8__TEXT9<__common__DATA @__picsymbolstub2__TEXT9<jV__la_sym_ptr2__DATA!?ABhu99__nl_symbol_ptr__DATA@ (Cr__textcoal_nt__TEXT@ 4C @yd PLL<0wuUS4"D$"D$ !D$"D$ "$>#D$ "$>t#D$ "$>!8!@@D$#D$ "$S>!D$#D$ "$->!D$#D$ "$>!D$$D$ "$=)!@D$$D$ "$=T"D$1$D$ "$=!@@D$G$D$ "$d=|"8t'!8u ]$E e$EEE m$EED$r$D$ "$="D$$D$ "$<"D$$D$ "$<,"D$$D$ "$<`"D$$D$ "$h<4[]ÐUSDL8p=@$<\$ D$L"D$d$<8u"D$d$;"D$d$;8dD$$8D$ D$D$\D$D$ @@D$ @@D$ @@D$l=$:($:EdD$$8D$ D$D$\D$D$E@@D$ E@@D$E@@D$l=$[:E$:D$#D$d$\:8uRd$9dD$=$9D$#D$d$98l=@E}us\=D$\D$ED$ D$ED$@$8E}u'dD$E@$8E$9녍D$#D$d$A98uVdD$ D$X=D$l=$%8D$#D$d$88uBdD$p=$7D$#D$d$8D[]USt9$Y79$079$7[]ÐUS,8u$6$7<$6H$W6$.6[]US$h@$5$5Eh$5hE$[]USdh488D$@D$<D$4D$08D$,D$(D$$8D$ p؉D$h؉D$`D$xD$8D$ 8D$D$<$488D$0D$,D$$D$ D$D$D$xD$8D$ 8D$D$D$3888u E48tB@D$ D$D@D$8$c38M@D$ <@@D$<@@D$8$38EEd[]UVS0 Ek$2oo8u!kD$$u2E8tLD$$02t 8x!D$+$2E D$$1u!D$k$1ED$$1u!D$k$1E8tLD$$[1t 8x!D$$I1E$18u&ED$ $18u8u8u 8u@@ D$D$$70E}u E$1E8uq;~&D$D$K$0@$0$t0E썃$0E8u6@@p@@$7/F8tLD$$Z/t 8x!D$$H/E8tLD$$/t 8x!D$$.E87o8t7o8t,o8t!kD$+$.E$ .8u&ED$$Y.8u8u8u 8u@@ D$D$$C-E}u E $/E$,8u&D$$e-E$,8t.@$J,0$,F8uD$$,/D$ D$oD$$+D$K$q+uOMD$K$E+uO!KD$ $E,E8t?D$$,u!D$K$+Ew8tw$*sC8uwvw{w$O*scD$[$*u![D$$R+E3D$+$)u%3D$$+ECD$;$)u%CD$$*E$>)8u!ED$$*$(8u!ED$ $E*1 D$$(#8u!D$K $*E4(' (76768uo $)EC$'36$';63D$;6$?'E0[^]ÐU#ÐUSpeD$ D$D$x,@X$E+D$x,@X$(+pD$x,@X$ +D$x,@X$*D$x,@X$*pD$x,@X$*D$x,@X$*D$x,@X$z*D$x,@X$]*0D$x,@X$@*pD$x,@X$#*D$D$x,@X$)D$x,@X$)$?:%US D$ d D$OD$E$)D$E$)VD$E$o)|D$E$Z)D$E$E)D$E$0)<D$E$)|D$E$)D$E$(D$E$(D$E$(\D$E$( D$D$E$( D$D$E$p( D$D$E$O("D$E$:(<D$E$%(D$E$(D$E$' D$D$E$' D$\D$E$' D$D$E$'D$E${' D$<D$E$Z'rD$E$E'D$E$0'D$E$'D$E$'\D$E$&D$E$&D$E$&<D$E$&|D$E$&H D$D$E$|&P D$D$E$[&E$!E$|!D$E$0&$?!US$D$ D$ D$ D$D$E$%D$E$%0D$E$%pD$E$%D$E$%0D$E$p%D$E$[%$? US$8T D$ D$E D$E$ E D$E$D$E D$E$E}t 4ED$E D$E$wE}t 4ED$E D$E$GE}t <ED$E D$E$E}t E D$E D$E$E}t <ED$E D$E$E}t ,ED$E D$E$E}t ,ED$E D$E$WE}t ED$E D$E$'E}t $ED$E D$E$E}t ED$E D$E$E}t ED$E D$E$E}t DE%D$E D$E$gE}t xE*D$E D$E$7E}t E.D$E D$E$u 4D$E D$E$E}t E:D$E D$E$u?D$E D$E$Xu?8uX$(D$E D$E$E}t XED$E D$E$E}t hE D$E D$E$u D$E D$E$ku D$E D$E$>t D$E D$E$t D$E D$E$t D$E D$E$t D$E D$E$t D$E D$E${E}t ED$E D$E$2t D$E D$E$E}t ED$E D$E$E}t EE D$E$}tb$EE;E|>UЍE D$MD$@&$E 8uD8u98u.8u#8uE 8uU U uT$s8uZum$L_u$58u3um$!u$$[]"" """{Gz?"{Gz?""?""2"8estwise122-0.01syn1.0default50//unreleased$Name: wise2-2-0 $%s %s (%s release) This program is freely distributed under a GPL. See source directory Copyright (c) GRL limited: portions of the code are from separate copyrights Query protein: %s Comp Matrix: %s Gap open: %d Gap extension: %d Query model: %s Start/End %s Target Sequence %s reverseforwardbothStrand: %s Codon Table: %s Subs error: %2.2g Indel error: %2.2g Algorithm %s %s output Score %4.2f bits over entire alignment Score reported as bits over a synchronised coding sequence model Score reported as bits over a flat random model %s String %s was unable to converted into a start/end policy Could not make %s out as target startCould not make %s out as gap penalty (must be integer at the moment)Could not make %s out as target endCould not read cdnaomic sequence in %sYou have already reversed the DNA by using %d - %d truncation. Re-reversingCould not make %s out as query startCould not make %s out as query endProteins can only have local/global startend policies set, not %sCould not read Protein sequence in %sCould not read hmm from %s Could not read %s as a hmmflatCannot interpret [%s] as a null model string Could not get maximum main_block number %s312L312Could not convert %s to a doubleCould not read Comparison matrix file in %sCould not read codon table file in %sWCould not open %s as an output fileNo random model. Ugh!codon.tableblosum62.bla%s (%s) This program is freely distributed under a GPL. See -version for more info Copyright (c) GRL limited: portions of the code are from separate copyright estwise in fasta format Options. In any order, '-' as filename (for any input) means stdin Dna [-u,-v,-trev,-tfor,-both,-tabs] Protein [-s,-t,-g,-e,-m] HMM [-hmmer,-hname] Model [-codon,-subs,-indel,-null] Alg [-kbyte,-alg] Output [-pretty,-para,-sum,-alb,-pal,-block,-divide] Standard [-help,-version,-silent,-quiet,-errorlog] For more help go %s -help. See WWW help at http://www.sanger.ac.uk/Software/Wise2/ Dna sequence options -u start position in dna -v end position in dna -trev reverse complement dna -tfor use forward strands only -both [default] do both strands -tabs Positions reported as absolute to DNA Protein comparison options -s start position in protein -t end position in protein -[g]ap [%3d] gap penalty -[e]xt [%3d] extension penalty -[m]atrix [%s] Comparison matrix HMM options -hmmer Protein file is HMMer file (version 2 compatible) -hname Name of HMM rather than using the filename Model options -init [%s] [default/global/local/wing] start end policy of HMM/protein match -subs [%2.2g] Substitution error rate -indel [%2.2g] Insertion/deletion error rate -null [syn/flat] Random Model as synchronous or flat [default syn] -alln [%s] Probability of matching a NNN codon Algorithm options -alg [333,333L,312,312L,333F] Algorithm used Output options [default -pretty -para] -pretty show pretty ascii output -para show parameters -sum show summary information -pep show protein translation, splicing frameshifts -alb show logical AlnBlock alignment -pal show raw matrix alignment -block [%s] Length of main block in pretty output -divide [%s] divide string for multiple outputs Jan 1 2008%s Version: %s Released: %s Compiled: %s This program is freely distributed under a Gnu Public License The source code is copyright (c) GRL 1998 and others There is no warranty, implied or otherwise on the performance of this program For more information read the GNULICENSE file in the distribution Credits: Ewan Birney wrote the core code. Portions of this code is from HMMer2, written by Sean Eddy gapgextinitematrixmstuvcodonnullalghmmerhnametrevtforYou have specified both trev and tfor. Interpreting as both strandssubsindeltabsprettyparasumpepalballnpaldivideblockWrong number of arguments (expect 2)! Arg line looked like (after option processing) %s Could not build objects!Could not build alignment!Could not show alignment. Sorry!?k⍀PWRw⍀wP>9b⍀bP% M⍀MP 8⍀8P#⍀#P⍀P⍀P⍀P⍀Pvq⍀P]X⍀PD?⍀P+&{⍀{P f⍀fPQ⍀QP<⍀<P'⍀'P⍀P⍀P|w⍀Pc^⍀PJE⍀P1,⍀P⍀P⍀Pj⍀jPU⍀UP@⍀@P+⍀+P}⍀Pid⍀PPK⍀P72⍀P⍀P⍀P⍀P⍀Pn⍀nPY⍀YPD⍀DPoj/⍀/PVQ⍀P=8⍀P$⍀P ⍀P⍀P⍀P⍀P⍀Pr⍀rPup]⍀]P\WH⍀HPC>3⍀3P*%⍀P ⍀ P⍀P9999::3:L:e:~::::::;-;F;_;x;;;;;;<'<@<Y<r<<<<<<=!=:=S=l======>>4>M>f>>>>>>>?$Ë $Ë$Õ!!`9!~!v!59l!g!]!"W!O!`9E!@!8!59.!)!!"!!9! ! ! ! ! " x" |" p" t" x"| "v i Y @O 9"  8 "8"8p"v8kP"\F8:t"08|"8"8"{8x"jt8^!S=o81"&y$0"i8 "d8!""| 8q!fP8D!8"-8 !7!7l"7@"pZ7O "@*7!7!7!7!j7_!P:7/!  7"7`"7"z7o!`J7?!07" "" 7 7p6j[`6UF 6@15+5!""w5 `-D@5D"Dy5Dm"DgX4DRC4D=. 4D(3D3D`3D 3D2D2D2DP"Dz 2Dte1DU8"DO@1D0("D*@1D`"D 1D0D0Df0D@0D!D0Dy"Dsd/DX"DRC/D=.`/D(:/D/D.D.D@.D.D-D-Dq`+Dk\*DP!DF"D@ 3'@`- @5-!@-@,@,}@sG,m`@V+,PC@9,3&@+ @`+@+@*@*!" y*cs!ckz*ce "c_ G=0@ -(" %0@ " (@ 8" d* ,@ ,@ " @* " " w" m&* g_* S " ?" 7- " ') ! ! ! ) 8" 0" 8" ) (" {q " g(" ZR) FP" <2P" (X" h" l" p) l" k) l" ! h" l" l" @) " " " t" g_) S@" ED" ;1@" '( D" @" " ! d" 9 ( ! ! ! ! t! i! cY! G?( 3! (! ! ! ! ! ! ! ! ! ! ! ! y! i! ^! SK( ?! +! #!  ( `" d" d" d" !  ' ! !  ! | ! q ! d \ ' P ! C ! 9 / ! % !  !   ! ! ! ! !  !   !  @' ! z ! n ! h ! ] ! R ! L B ! *  !  !  ! ! ! ! ! ! ! !  ' ! ! z p ! c [ & O ! B ! 8 . ! $ !  !  `& "  " "  `& !  ! "  & z ! m ! c Y ! O ! D ! 7 / % # `"  d"  d"   `"  4@  @ ! ! ! 4@{ q @b !K !@ !) @! @  ! !(@0@""h"D"H"X""$@| @tj!^!R(@F0@:".! ""d""h",@D"X""$@! }!Hwm!Hg_WJ!HD -#!" "!!! 4@$@ @ qg"]%Q"KA$@5"*p"$"%" @ @"t""%"|"k^!<"0@ @ |""%"4@""""%"wm @:!.""h""! @!!!!"q"^h"R"C!=3")%!" @%D""%!$@x" " $ |l" vl" b$ R8" LB" 8$ ((" "" $  " " ~$ y$ q$ i$ ! " " S$ z! tj" `=$ T`" ND" :'$ +! #" $ " " # " " # ! " # ! |! vl" b# \R" H # B8" .# "! " "  xl\T @ ?@ ?y t n?>f?>` [ U?>M?>G B <?>4?>. ) #?>?>  ?>?>  ?w>?w>  ?^>?^>  ?E>?E>  ?,>?,>  ?>?> z t?=l?=f a [?=S?=M H B?=:?=4 / )?=!?=  ?=?=  ?}=?}=  ?d=?d=  ?K=?K=  ?2=?2=  ?=?=  z?=r?=l g a?<Y?<S N H?<@?<: 5 /?<'?<!  ?<?<  ?<?<  ?j<?j<  ?Q<?Q<  ?8<?8<  ?<?<  ?<x?<r m g?;_?;Y T N}?;F}?;@ ; 5y?;-y?;' " u?;u?;  q?;q?;  m?p;m?p;  i?W;i?W;  e?>;e?>;  a?%;a?%;  ]? ;~]? ;x s mY?:eY?:_ Z TU?:LU?:F A ;Q?:3Q?:- ( "M?:M?:  I?:I?: E?v:E?v: A?]:A?]: =?D:=?D: 9?+:9?+: 5?:5?:~ y s1?9k1?9e ` Z-?9R-?9L G A)?99)?93 . (%?9 %?9  !?9!?9 |xtplhd`\XTPLHD@<840,($  Y{zyh|TvtwZ[WQimldSqxVXN~noe}OMLUpca]b^_\ugPrs`kjRY{zyh|TvtwZ[WQimldSqxVXN~noe}OMLUpca]b^_\ugPrs`kjRRf; @J @ @t @h"l"X"wP"X !0@ "(@"'"!"3"""TH"~"!x!!18"#0"5" "!!y4@>@"""o$@s!!e!!!!!G!<,@"gL"t"p"8"b"9|"x" 'd"`"("  "P!A!7!!/!#!KD"\!}WJ*3rk#sC_O '*M c y] ' Iml S_program_name_dna_seq_file_cdna_tstart_str_tstart_tend_str_tend_reverse_target_abs_use_tsm_protein_file_pro_hmm_file_tsm_hmm_name_qstart_str_qstart_qend_str_qend_matrix_file_mat_gap_str_gap_ext_str_ext_codon_file_ct_output_file_ofp_rmd_subs_string_subs_error_indel_string_indel_error_null_string_use_syn_force_flat_insert_should_set_hmm_allN_string_allN_startend_string_startend_alg_alg_str_show_PackAln_show_AlnBlock_show_pretty_show_pep_show_para_show_match_sum_do_both_main_block_str_main_block_divide_str_dpri_show_parameters___i686.get_pc_thunk.bx_show_output_pal_alb_mss_free_temporary_objects_free_io_objects_reverse_target_build_alignment_rm_cm_cp_build_objects_build_defaults___i686.get_pc_thunk.cx_show_short_help_show_help_show_version_main___i686.get_pc_thunk.axdyld_stub_binding_helper___sF_Wise2_Score2Bits_Wise2_is_random_AlnColumn_genewise_Wise2_fatal_Wise2_strip_out_remaining_options_with_warning_Wise2_strip_out_boolean_argument_Wise2_strip_out_assigned_argument_Wise2_new_DPRunImpl_from_argv_Wise2_strip_out_standard_options_Wise2_bootstrap_HMMer2_Wise2_show_standard_options_Wise2_show_help_DPRunImpl_exit_Wise2_sprinkle_errors_over_CodonMapper_Wise2_flat_CodonMapper_Wise2_flat_cDNAParser_Wise2_default_RandomModel_Wise2_RandomModelDNA_std_Wise2_openfile_Wise2_read_CodonTable_file_Wise2_read_Blast_file_CompMat_Wise2_is_double_string_Wise2_alg_estwrap_from_string_strcmp_Wise2_set_startend_policy_ThreeStateModel_Wise2_stringalloc_Wise2_ckfree_Wise2_display_char_in_ThreeStateModel_Wise2_HMMer2_read_ThreeStateModel_Wise2_truncate_Protein_Wise2_read_fasta_file_Protein_strlen_Wise2_truncate_cDNA_Wise2_read_fasta_file_cDNA_Wise2_is_integer_string_Wise2_warn_Wise2_threestatemodel_mode_from_string_Wise2_MatchSummarySet_from_AlnBlock_estwise_Wise2_AlnBlock_from_TSM_estwise_wrap_Wise2_AlnBlock_from_Protein_estwise_wrap_Wise2_cDNA_from_Sequence_Wise2_reverse_complement_Sequence_Wise2_free_cDNA_Wise2_free_RandomModelDNA_Wise2_free_CodonTable_Wise2_free_ThreeStateModel_Wise2_free_MatchSummarySet_Wise2_free_PackAln_Wise2_free_AlnBlock_Wise2_show_simple_PackAln_Wise2_mapped_ascii_AlnBlock_Wise2_write_fasta_Sequence_Wise2_Protein_from_GeneWise_AlnColumn_Wise2_show_MatchSummarySet_estwise_Wise2_show_MatchSummary_estwise_header_Wise2_free_Protein_Wise2_pseudo_Protein_from_ThreeStateModel_Wise2_protcdna_ascii_display_fprintf