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"߾׼X׸P׶H߼0߰߱ߴ ߷ߣ('``%S% %@%`y%&R0&RP&R& *s %@(%X`0% -b8%%&(* F #2 8CR0&RP&t %&8CR0&RP&- %&R0&RP&7 %&3DSMDD @*FHH!F!!%F% 2E&s %@(%\`0% .(8%|ZF րD(F:)E!! ߿߼' ߿߼''8%@DF aF<$!F,>F `E!!F aF aׁP$F!1>E/ׂ$F&E `4$$ԧԩԮHF&J@M;ԨԭPM 2!M3aԤԬXL1!M3!ԣԫ`Ld0Ml2ԢԪhLC0MK2ԡԩpL"0aM*2aԠԨxL0!M 2!F 0ԧԩF(2F(9F J@xp"F)9׈X F&B'dH /׊XF*׋F+R@F*ZF+JB0F K ׬0F,c( F cר(F Bׇ߿Hץ F(9׀h$F ,<l($׉ F)-EF F&2׉0F*JC4$$ԧԣԬF)M;!ԢԫLCHMlJԡԪL"HaMKJԠԨLH!M J!ׇHF Hԫ ԪF(JF(RF*JF ZF+RF*9xpF&9׋X F&Z'dH /׎XF.׏F/s@F.{F/kB0F k ׬0F,c F cרF B߿Hׇץ F(9I߷8H ׉F H߷8߿H߼@'P׊8F'Q߷8DF'QF 8߼@'P׈XF%B'dH /׌XF,׫ F+bF,ZF+RF,c  ׬עF M!ׁF!߷8߿H߼@'P߷8׀@F'߼@'P\$ׁ(F&>EX$ׂ F&>ElF&2ׇHPF&9߼@߷8F 8'P'<$!!!h 0(%߿߼''<$!А!!h 0$߿߼''<$!X!!h 0$߿߼'Weighbor ver 1.2.1 [ 3-Jul-01] usage: weighbor [-L num] [-b num] [-i name] [-o name] [-v[v[v]]] [-V] -L num set the sequence length to num (default %g) -b num set number of bases (default %g) -i name read input from file -o name write output to file -v turn on logfile and dump level 1 info -vv turn on logfile and dump level 2 info -vvv turn on logfile and dump level 3 info -V print version information For those using this program for research please use the following citation for this program: Bruno, W. J., Socci, N. D. and Halpern, A. L., ``Weighted Neighbor Joining: A Fast Approximation to Maximum-Likelihood Phylogeny Reconstruction,'' Molecular Biology and Evolution, 17(1): 189-197, (2000). Advance (expert) options [-XqrzSTeZ] -X turn on expert mode (allows use of these options) n change normalization of R(i,j,j') q turn off q[q[i]]==i checking r turn on recalculation of Delta B z use the old (N^3) method to calculate z(i,j) S use barred version of sigma for R(i,j,j') T use unbarred versions of d, Delta B and S for R(i,j,j') e extended tournament option w turn on non-deterministic warnings x change normaliztion of R(i,j) Z Calculate PQNew and sigmaNew for z-score *<%%%%%%%%%(%)%%%%%%%%%)@%%%%%%(%%%%%(%%%%%%(Must specify a number greater than zero eg: -b 2.3 Note the space after the `b' Expert Option [%c] +x+l*****+X**********+********+P**+D+8****+,+ *+Must specify a length eg: -L 1000 Note the space after the `L' No length was set. Using the default L=%g WARNING: Not recommended that you use the -Xr and -Xn flags together ERROR: B must be greater than 1.0 now set to %.15g WARNING: weighbor is not expected to work for values of b close to 1.0 You have set b to %.15g weighbor.outweighbor::main::open(outfile) ============================================ L = %g, b = %g Input Distance Matrix = (%s:%f,%s:%f) (%s:%f,%s:%f) weighbor::tree::createNodeweighbor::tree::createRootNodeALGORITHM ERROR Can not call moveMem with overlapping blockswhere src is less than destination weighbor:tree:moveMem FATAL ERROR--Out of static space weighbor:tree:wrapPrint:: length=%d weighbor::matrix::matrix(1)weighbor::matrix::matrix(2)weighbor::matrix::vector%10.7f, %10.7f; %10.7f] %s could not be open for reading %s could not be open for writing weighbor::io::openWriteweigbor::ioInvalid PHYLIP file format. First line must be contain one integer. The current line is File format error-Out of memoryFile format error-2Setting max length to MAXD=%g Double precision arithmetic is insufficient for the current values of N=%d, L=%g, and d_MAX=%g Maybe try the N^4 version of weigbor setting variance bounds to %g ... %g build::buildTree:out of memory-q build::buildTree:out of memory-q2 build::buildTree:out of memory-nodesq[%d]=%d R(%d,%d)=%g ij=%d,%d k=%d q[k]=%d minR = %.16g R[k] = %.16g No pair with q[q[i]]==i The pair does not satisfy q[q[i]]==i (checking is off)Extended Tournament New Winner(A): (%d, %d) R=%g Extended Tournament New Winner(B): (%d, %d) R=%g R=%g, R1=%g, R2=%g warning: tie scores encountered; topology may depend on sequence order! taxon %s and taxon %s Join taxon %s to taxon %s (%s next best choice) p-value = %g Join taxon %s to taxon %s; R=%g Second best pair (%s, %s); R=%g No second best pair Renormalizing z[%d,%d] = %g phi=%g dBar_iip=%g WARNING: Negative branch length %g set to zero \bar b_[%d%d] = %g b_[%d%d]=%g \bar b_[%d%d] = %g b_[%d%d]=%g Reduced d_ij= build::buildTree:out of memory-rootERROR: sigma_na(%g,%g)=%g < 0.0 | X+Y=%g %12g - %12g - %12g sig4=%g (%d,%d,%d,%d) %g-%g-%g-%g PQ=%g iP=%g jP=%g Qk=%g d(ik)=%g d(jk)=%g sigord=%g (%d,%d,%d,%d) %g+%g-%g+%g+%g-%g PQ=%g iP=%g jP=%g Norm < 0 i=%d j=%d jp=%d norm=%g sigs %g %g basics: WARNING: non-transitive R(i,j,j'); tree could depend on input order New winner %d (orig winner was %d) WARNING: Tie in R(i,j,j'); tree likely to depend on input order Tie %d==%d i=%d q[i]=%d q2[i]=%d minR=%f z(%d,%d)=%g Previous pair (%d,%d)-->%d i %d j %d k %d weight %f s_ij %f s[i][j]>0.0Round off error in the calculation of s_ij and/or delta^2B_ij. Can not use the N^3 version of weighbor for this tree Delta b_{ij}= Delta^2 b_{ij}= s_{ij}= Recalc N %d i %d j %d k %d weight=%g sij=%g sigma %g %g [%g %g] deltaB %g %g sigPQ>0.0@@=-@@ I>C@\wNM6]@wÈR@S]?ǐZ1"@74/@n~U@ wR@8yB;? >@!,5@P @r)b@&+@0]@(!#ok@9[>Wp<_X@/}f@]li@rt@U좝&@5m@ |@޼? @9[_`?ӊxe?$%? .?xDŵ?E q,9?B}}?c!G%&J+]h}4xHX)P( YѠ Y Y|0 Y Y( YS YO"%-.`./0803 446677;@;H;X<<Hhi8jmoprPvy`pXPHŀŸ (048<@DHLPTX\ >. &֕??(\)?@4<?zG{UUUUUU@?UUUUUU>_@>P?6C->Ey0:栞f;??wr%7.4g (%s) (%s) %s %s, %s) %s:%f(,):%f); [%10.7f] r%s::%d io.cw%s %lf%7.4g c_i = %s::%d calcq.cargs: %f %f calcb.c%s::%d %9.4g l* { 6kv &  $ y z   C~~p)y  )y&6|~z !j) 4x   {  mmTx7}0' I w }vk  _ ! _"tak  t  t v ,!x }   y ~ |{~{~yxyy59]%a V|} !" }~}  }}%~!} CU      -  ! {  ! 5 ~  ~ ~ ~=y /tmp/Weighbor/usr/includenoise.cCweighbor.hMstdlib.hOstandards.hDsgidefs.h7locale_attr.hgetopt.h assert.h stdio.hohz  Y oq'y);3M2M3 '~!-yv ~~(> %~   v   x9Y ||||RB1 | = ~ $ f.grt6 yGa /tmp/Weighbor/usr/includecalcq.cestdio.howeighbor.hMsgidefs.h7standards.hDstdlib.hOlocale_attr.hgetopt.h assert.h y`h@ ff xxxxtnqooo~zzz~pppp}rrrsor}t t t q t tlx(v{ s }v{~~} w~ {~{{}5 ~1!8~5 qH4;|N%~DyyR N 8&  v ~  u   x  z z  c  z} }} z6|P$7 [$ g/$ n(9'-~|(3)<#3#3N  pz    N   d9E $ 1~ ~91*w /tmp/Weighbor/usr/includecalcb.c>stdio.howeighbor.hMsgidefs.h7standards.hDstdlib.hOlocale_attr.hgetopt.h assert.h  !) 0P " 8   $#r1 I~~5~~ Q~~~< A1PU,~PQs srrq$  ssXrX] *} *} *} |  | | $ ~{. #, ]   #mD2ssXrX] *} *} *} 1  /tmp/Weighbor/usr/includecalcz.cjweighbor.hMsgidefs.h7standards.hDassert.h stdio.hogetopt.h P |     _   ur || ( $  u    v zz=R&,}&,m|%Q&,Y  k  t 1  }:({{{  w   v # |`  Gll5 }6){{{  v   v #2K}yy||d}~}B~~~ ||}#=~~    |  )  u~~ w u( $  u    zzn&,}&,J=M|% &,0 n   /tmp/Weighbor/usr/includecalerf.casgidefs.h7standards.hDstdio.hogetopt.h %5 z%}{~|{~   u J }z|{z~ Hj!w~$zlLdd|+l   2 crtninit.s O __start_mcount__rld_obj_head__Argv__Argc __istart6ZusagetmainnodesmDvCmSmDelBmDel2BsdeltaBdelta2B*oldDeltaB?taMtb[tciLvEPSILONMINBBsigBisigBBsigBiBBLinvsigBBimaxVarminVaroutfile(printLevel>checkQQIRrecalcBeoldZflagyuseSigmaBaruseBarValuesextendedTournwarnFlagn_Flagw_Flagx_Flag ZZ_FlagexpertMode_RcreateNodeqcreateRootNodedeleteTreedeleteNodemoveMemwrapPrint printBinaryTree2printTreePVmatrixqfreeMatrixvectorfreeVectorsetMMdelRowColprintMatrix#printVectorCSQR\DMAXvDMINRECTK;NopenReadkopenWriteprintErrorreadPhylipFile* 7TbuildTreesmaxVectore Tsigma2tpsigma2tinvsigma2_3sigma_nasigma2_3psig4sigord. 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