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觍A>~nE~ E~e$$180DH蛌f$f.ڴv(D$E>C`0DH߸`H޿ 3=AH;$8D ШHAwD;$4D$dH$LD$ H$H=EHSAA+H=H$8t)H$8C8H$8L H$t$H$H$Lcu诌IL)5H$L$E1ExE~L$IcMjI\HHL`tHTL)%UL$IDI[AHf\$ 1L\$ 1kA$f\$ ~6fD%fD.fD-DX-fD.$D HEuTH$8t'H$8f$D2DUuAxAD;$H$1\$ nvH$H$f\$ H9IH4ׂCI)ILH?HH)i@BHcH$HH)H$H$II)I@B~9$L~%kMLHMBDCRI?LD陫 CLuB9$L~9LcOL$fL A'CػCݻC4D"I4ܹ!Cu 9$L]I4ܹ3Cu 9$LsMA :CLLtCCLLu H q@ 5D hA LCLLtVCLLu|鉪`CLu 9$L(MܹeCLuFDŽ$`F11Hcݺ I<{h$`Iܾh5D*AlCLLƄ$VL fA'CػCݻCqC11HcInRateCategories > 0%7i.%2.2i seconds: iNode < NJ->nSeq(End of file)parent >= 0child >= 0parents[child] < 0children[parent].nChild < 3oldn < pc->nChildRemoving node %d parent %d parents[node] >= 0pc->nChild + nc->nChild <= 3pc->nChild < 3nc->nChild<=2node >= 0fOut != ((void *)0)codeIn != 127 Cannot read %s Cannot read %d entry of %s Error reading %s nSibs==2NJ->parent[node] == NJ->rootOut of memory hash->buckets[hi].nCount == 0hash->buckets[hi].first >= 0m > 0 %c%dpos %d char %c code %d strlen(seq) == nPosRead distance matrix from %s Filename %s too long nUniqueSeq>0last>=0Empty myrealloc %d%d' (),: Error parsing header line:%s No sequence in phylip line %sError reading header line No name in phylip line %sError reading input file nSave > 0besthits[iBest].i == iNodenIn > 0nOut > 0iSave == nSavenBootstrap>0FreeUpProfiles -- freed %d aln != ((void *)0)('%s':0.0(%s:0.0,'%s':0.0,%s:0.0)%.3f:%.5f):%.5f'%s'); iName < unique->nSeq)%dnRateCategories >= 0Optimizing alpha round %dGamma%d Site LogLk r=%.3fGamma%d %d %.3fBoot%d %diter < 30transmat->stat[j] > 0transt[j][i] > 0tot > 0rate > 0nCodes==4total_rate > 1e-6lkAB > 0nCodes == 4PairLogLk(%.4f) = %.4f qo != ((void *)0)loglk < 1e100iFreqA == pA->nVectorsiFreqD == pD->nVectorsiFreqC == pC->nVectorsiFreqB == pB->nVectorsnBootstrap > 0iFreq==profile->nVectorsiFreq2 == profile2->nVectorsiFreq1 == profile1->nVectorsnVisible > 0Reset TopVisible: %d=>%dnVisible < nActiveiNode >= 0NJ->parent[iNode] < 0Updated TopVisible: %d=>%d:%.4ftophits != ((void *)0)NewVisible %d %d %f NJ->parent[hit->i] < 0nUnique < nCombinedbestjoin->j >= 0bestjoin->i == iNodel->hits != ((void *)0)l->nHits > 0bSuccessBetterI %d %d %d %d %f %f BetterJ %d %d %d %d %f %f bestJ.i == join->jbestI.i == join->iSetBestHit %d %d %f %f NJ->parent[node] < 02ndlevel1stlevelCombined %d ops so far %ld iNode>=0lNew->hits == ((void *)0)nSave>0lNew->hits != ((void *)0)2 * tophits->m <= NJ->maxnodenHitsOld <= tophits->mnUnique2 > 0nNewHits > 0iMerge == nMergenUnique > 0lSource->nHits > 0lSource->hitSource < 0Skipping seed %d Trying seed %d Replaced %ld top hit entries nCheck > 0nCheck <= lTarget->nHitscloseNode2 >= 0l->hits[0].j < NJ->nSeql->hits[0].j >= 0l->hits[0].j != iNode2 * tophits->m <= NJ->nSeqiWorst >= 0join->i >= 0 && join->j >= 0profiles != ((void *)0)distances != ((void *)0)nProfiles>1 && nProfiles <= 4AB|CDAC|BDAD|BC %d (%d/%d %d/%d %d/%d %d/%d)fPostTot > 1e-10node == NJ->rootnChild >= 2NJ->rates.nRateCategories > 0x > 0gtr->NJ != ((void *)0) %c:%fnActiveOld > 0iFreq2 == old2->nVectorsiFreqNew == new->nVectorsiFreqOut == out->nVectorsiFreq1 == old1->nVectorsAverage %d profiles Node %d outdist %f Made out-profile Made sequence profiles %c:%fNJ->child[node].nChild == 2upProfiles != ((void *)0)nodeABCD[2] >= 0NJ->child[node].nChild==2node != NJ->rootparents[i] >= 0parents[0] != parents[1]newAround[0] != newAround[1]MLME, %d changes (max delta %.3f)delta-loglk-deltaLenOld tree lk -- %.4f New tree lk -- %.4f Going up back to node %d ML Lengths %d of %d splitsnChild == 2 || nChild == 3NJ->child[parent].nChild==2GTRFreq %.4f %.4f %.4f %.4f c->nChild == 2move (%d,%d)%.4fnodeListLen == NJ->maxnodeRewinding SPR to %d abandonedNo '(' at startunexpected tokennew < maxnodesstack_size < maxnodesNJ->nSeq == unique->nUniquewhile reading parenthesesunbalanced parenthesesAdded %d to stack Changed root from %d to %d too many ')'unexpected '(' after ')'NJ->parent[NJ->root] < 0Joined %6d of %6dVisible %d %d %f %f Recomputing outprofile %d %d Top-hit-list size = %d of %d iOldVisible>=0visible[iNode].i == iNodenTop==3nSaved < nActive-1nSaved==nActive-1NJ->nSeq >= 1!(slow && m>0)NJ->nSeq == 2nTop <= 2-logdist-rawdist-makematrixCommand:Read alignmentHashed the names %d -verbose-quiet-noprSH-like %d+NNI (%d rounds)+SPR (%d rounds range %d)+ML-NNI (%d rounds) opt-each=%dstandard inputSSE32.1.4weightedbalancedAmino acidNucleotideStart at tree from %s %s %s Whelan-And-GoldmanJones-Taylor-ThortonML Model: %s,Constraints: %s Weight: %.3f -slow-fastestIdentified unique sequencesNJME_SPR%dME_LengthsME_NNI%d+2ndExhaustive (slow)FastestNormal (%d alignments)Generalized Time-ReversibleJukes-CantorRead the constraintsBLOSUM45%differentRead tree from %s unconstrained Worst %sdelta-%s %.3fTreeCompleted %.2fLocal boot %dNo alignment sequences -2nd-no2nd star-only %ldML_Lengths%dML_NNI%d (converged) (final)~ML_LengthsTreeLogLk ML_Lengths%d %.4f Cannot write to: %s -slownninCodes==20-matrix-nomatrix-quote-intree-intree1-bionj-boot-noboot-nosupport-seed-top-notop-topm-close-refresh-nni-spr-sprlength-mlnni-noml-mllen-nome-help-expert-pseudo-constraints-constraintWeight-mlacc-exactml-mlexact-approxml-mlapprox-cat-nocat-wagFastTree %s %s%s: %sIlllegal -mlacc argument: %s -gtr-gtrrates-gtrfreq-log-gamma-C6 ?-C6?MbP?9B.?Uk"@@-C6?LogMLRatesNGapsReadTreeAddChildReadTreeMaybeAddLeafReadTreeRemoveTraversePostorderAddToFreqReplaceChildSiblingRootSiblingsmymallocMakeHashtableInitTopHitsSeqToProfileAlnToConstraintsUniquifyAlnmyreallocReadAlignmentSortSaveBestHitsSHSupportDeleteUpProfileFreeAlignmentSeqsPrintNJAllocRateCategoriestqliCreateTransitionMatrixCreateGTRPairLogLkPairNegLogLkProfileDistPieceSplitSupportSetCodeDistProfileDistSetOutDistanceSetCriterionResetTopVisibleTransferBestHitsUpdateTopVisibleUpdateVisibleUniqueBestHitsGetBestFromTopHitsTopHitNJSearchSetBestHitTopHitJoinSetAllLeafTopHitsFastNJSearchExhaustiveNJSearchCorrectedPairDistancesPosteriorProfileTreeLogLkMLSiteLikelihoodsByRateSetMLRatesGTRNegLogLkMLQuartetOptimizeUpdateOutProfileOutProfileAverageProfileGetUpProfileSetupABCDRecomputeProfileUpdateForNNIUnwindSPRStepFindSPRStepsOptimizeAllBranchLengthsSetMLGtrSetProfileSPRReadTreeFastNJmainnodefaultnone(no NNI)(no SPR)(no ML-NNI)FastTree [-nt] [-n 100] [-quote] [-pseudo | -pseudo 1.0] [-boot 1000 | -nosupport] [-intree starting_trees_file | -intree1 starting_tree_file] [-quiet | -nopr] [-nni 10] [-spr 2] [-noml | -mllen | -mlnni 10] [-mlacc 2] [-cat 20 | -nocat] [-gamma] [-slow | -fastest] [-2nd | -no2nd] [-slownni] [-seed 1253] [-top | -notop] [-topm 1.0 [-close 0.75] [-refresh 0.8]] [-matrix Matrix | -nomatrix] [-nj | -bionj] [-wag] [-nt] [-gtr] [-gtrrates ac ag at cg ct gt] [-gtrfreq A C G T] [ -constraints constraintAlignment [ -constraintWeight 100.0 ] ] [-log logfile] [ alignment_file ] > newick_tree or FastTree [-nt] [-matrix Matrix | -nomatrix] [-rawdist] -makematrix [alignment] [-n 100] > phylip_distance_matrix FastTree supports fasta or phylip interleaved alignments By default FastTree expects protein alignments, use -nt for nucleotides FastTree reads standard input if no alignment file is given Input/output options: -n -- read in multiple alignments in. This only works with phylip interleaved format. For example, you can use it with the output from phylip's seqboot. If you use -n, FastTree will write 1 tree per line to standard output. -intree newickfile -- read the starting tree in from newickfile. Any branch lengths in the starting trees are ignored. -intree with -n will read a separate starting tree for each alignment. -intree1 newickfile -- read the same starting tree for each alignment -quiet -- do not write to standard error during normal operation (no progress indicator, no options summary, no likelihood values, etc.) -nopr -- do not write the progress indicator to stderr -log logfile -- save intermediate trees so you can extract the trees and restart long-running jobs if they crash -log also reports the per-site rates (1 means slowest category) -quote -- quote sequence names in the output and allow spaces, commas, parentheses, and colons in them but not ' characters (fasta files only) Distances: Default: For protein sequences, log-corrected distances and an amino acid dissimilarity matrix derived from BLOSUM45 or for nucleotide sequences, Jukes-Cantor distances To specify a different matrix, use -matrix FilePrefix or -nomatrix Use -rawdist to turn the log-correction off or to use %different instead of Jukes-Cantor -pseudo [weight] -- Use pseudocounts to estimate distances between sequences with little or no overlap. (Off by default.) Recommended if analyzing the alignment has sequences with little or no overlap. If the weight is not specified, it is 1.0 Topology refinement: By default, FastTree tries to improve the tree with up to 4*log2(N) rounds of minimum-evolution nearest-neighbor interchanges (NNI), where N is the number of unique sequences, 2 rounds of subtree-prune-regraft (SPR) moves (also min. evo.), and up to 2*log(N) rounds of maximum-likelihood NNIs. Use -nni to set the number of rounds of min. evo. NNIs, and -spr to set the rounds of SPRs. Use -noml to turn off both min-evo NNIs and SPRs (useful if refining an approximately maximum-likelihood tree with further NNIs) Use -sprlength set the maximum length of a SPR move (default 10) Use -mlnni to set the number of rounds of maximum-likelihood NNIs Use -mlacc 2 or -mlacc 3 to always optimize all 5 branches at each NNI, and to optimize all 5 branches in 2 or 3 rounds Use -mllen to optimize branch lengths without ML NNIs Use -mllen -nome with -intree to optimize branch lengths on a fixed topology Use -slownni to turn off heuristics to avoid constant subtrees (affects both ML and ME NNIs) Maximum likelihood model options: -wag -- Whelan-And-Goldman 2001 model instead of (default) Jones-Taylor-Thorton 1992 model (a.a. only) -gtr -- generalized time-reversible instead of (default) Jukes-Cantor (nt only) -cat # -- specify the number of rate categories of sites (default 20) -nocat -- no CAT model (just 1 category) -gamma -- after the final round of optimizing branch lengths with the CAT model, report the likelihood under the discrete gamma model with the same number of categories. FastTree uses the same branch lengths but optimizes the gamma shape parameter and the scale of the lengths. The final tree will have rescaled lengths. Used with -log, this also generates per-site likelihoods for use with CONSEL, see GammaLogToPaup.pl and documentation on the FastTree web site. Support value options: By default, FastTree computes local support values by resampling the site likelihoods 1,000 times and the Shimodaira Hasegawa test. If you specify -nome, it will compute minimum-evolution bootstrap supports instead In either case, the support values are proportions ranging from 0 to 1 Use -nosupport to turn off support values or -boot 100 to use just 100 resamples Use -seed to initialize the random number generator Searching for the best join: By default, FastTree combines the 'visible set' of fast neighbor-joining with local hill-climbing as in relaxed neighbor-joining -slow -- exhaustive search (like NJ or BIONJ, but different gap handling) -slow takes half an hour instead of 8 seconds for 1,250 proteins -fastest -- search the visible set (the top hit for each node) only Unlike the original fast neighbor-joining, -fastest updates visible(C) after joining A and B if join(AB,C) is better than join(C,visible(C)) -fastest also updates out-distances in a very lazy way, -fastest sets -2nd on as well, use -fastest -no2nd to avoid this Top-hit heuristics: By default, FastTree uses a top-hit list to speed up search Use -notop (or -slow) to turn this feature off and compare all leaves to each other, and all new joined nodes to each other -topm 1.0 -- set the top-hit list size to parameter*sqrt(N) FastTree estimates the top m hits of a leaf from the top 2*m hits of a 'close' neighbor, where close is defined as d(seed,close) < 0.75 * d(seed, hit of rank 2*m), and updates the top-hits as joins proceed -close 0.75 -- modify the close heuristic, lower is more conservative -refresh 0.8 -- compare a joined node to all other nodes if its top-hit list is less than 80% of the desired length, or if the age of the top-hit list is log2(m) or greater -2nd or -no2nd to turn 2nd-level top hits heuristic on or off This reduces memory usage and running time but may lead to marginal reductions in tree quality. (By default, -fastest turns on -2nd.) Join options: -nj: regular (unweighted) neighbor-joining (default) -bionj: weighted joins as in BIONJ FastTree will also weight joins during NNIs Constrained topology search options: -constraints alignmentfile -- an alignment with values of 0, 1, and - Not all sequences need be present. A column of 0s and 1s defines a constrained split. Some constraints may be violated (see 'violating constraints:' in standard error). -constraintWeight -- how strongly to weight the constraints. A value of 1 means a penalty of 1 in tree length for violating a constraint Default: 100.0 For more information, see http://www.microbesonline.org/fasttree/ or the comments in the source code FastTree protein_alignment > tree FastTree -nt nucleotide_alignment > tree FastTree -nt -gtr < nucleotide_alignment > tree FastTree accepts alignments in fasta or phylip interleaved formats Common options (must be before the alignment file): -quiet to suppress reporting information -nopr to suppress progress indicator -log logfile -- save intermediate trees, settings, and model details -fastest -- speed up the neighbor joining phase & reduce memory usage (recommended for >50,000 sequences) -n to analyze multiple alignments (phylip format only) (use for global bootstrap, with seqboot and CompareToBootstrap.pl) -nosupport to not compute support values -intree newick_file to set the starting tree(s) -intree1 newick_file to use this starting tree for all the alignments (for faster global bootstrap on huge alignments) -pseudo to use pseudocounts (recommended for highly gapped sequences) -gtr -- generalized time-reversible model (nucleotide alignments only) -wag -- Whelan-And-Goldman 2001 model (amino acid alignments only) -quote -- allow spaces and other restricted characters (but not ' characters) in sequence names and quote names in the output tree (fasta input only; FastTree will not be able to read these trees back in -noml to turn off maximum-likelihood -nome to turn off minimum-evolution NNIs and SPRs (recommended if running additional ML NNIs with -intree) -nome -mllen with -intree to optimize branch lengths for a fixed topology -cat # to specify the number of rate categories of sites (default 20) or -nocat to use constant rates -gamma -- after optimizing the tree under the CAT approximation, rescale the lengths to optimize the Gamma20 likelihood -constraints constraintAlignment to constrain the topology search constraintAlignment should have 1s or 0s to indicates splits -expert -- see more options For more information, see http://www.microbesonline.org/fasttree/ Distance matrix entry %d,%d should be %f but eigen-representation gives %f Distance matrix not symmetric for %d,%d: %f vs %f /usr2/people/mprice/Genomics/stat/FastTree.cToken too long in tree file, token begins with %s Tree parse error: unexpected token '%s' -- %s iSeqNonunique >= 0 && iSeqNonunique < unique->nSeqiSeqUnique >= 0 && iSeqUnique < unique->nUniqueSkipped redundant leaf uniq%d name %s Found leaf uniq%d name %s child of %d not recognized as a sequence nameRepointing parent %d to child %d Constraint Penalties at %d: ABvsCD %.3f ACvsBD %.3f ADvsBC %.3f %d/%d %d/%d %d/%d %d/%d Total Constraint Penalties: ABvsCD %.3f ACvsBD %.3f ADvsBC %.3f Header line in %s has too many entries Header line in %s should be tab-delimited Header line %s in file %s does not have expected code %c # %d in %s Cannot parse field %s in file %s Cannot read line %d from file %s Header line in %s ends prematurely Error reading header line for %s: %s NJ->child[NJ->root].nChild == 3((((unsigned long) new) & 15L) == 0L)__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p (hash->buckets[hi].string) && __builtin_constant_p (strings[i]) && (__s1_len = strlen (hash->buckets[hi].string), __s2_len = strlen (strings[i]), (!((size_t)(const void *)((hash->buckets[hi].string) + 1) - (size_t)(const void *)(hash->buckets[hi].string) == 1) || __s1_len >= 4) && (!((size_t)(const void *)((strings[i]) + 1) - (size_t)(const void *)(strings[i]) == 1) || __s2_len >= 4)) ? __builtin_strcmp (hash->buckets[hi].string, strings[i]) : (__builtin_constant_p (hash->buckets[hi].string) && ((size_t)(const void *)((hash->buckets[hi].string) + 1) - (size_t)(const void *)(hash->buckets[hi].string) == 1) && (__s1_len = strlen (hash->buckets[hi].string), __s1_len < 4) ? (__builtin_constant_p (strings[i]) && ((size_t)(const void *)((strings[i]) + 1) - (size_t)(const void *)(strings[i]) == 1) ? __builtin_strcmp (hash->buckets[hi].string, strings[i]) : (__extension__ ({ __const unsigned char *__s2 = (__const unsigned char *) (__const char *) (strings[i]); register int __result = (((__const unsigned char *) (__const char *) (hash->buckets[hi].string))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((__const unsigned char *) (__const char *) (hash->buckets[hi].string))[1] - __s2[1]); if (__s1_len > 1 && __result == 0) { __result = (((__const unsigned char *) (__const char *) (hash->buckets[hi].string))[2] - __s2[2]); if (__s1_len > 2 && __result == 0) __result = (((__const unsigned char *) (__const char *) (hash->buckets[hi].string))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p (strings[i]) && ((size_t)(const void *)((strings[i]) + 1) - (size_t)(const void *)(strings[i]) == 1) && (__s2_len = strlen (strings[i]), __s2_len < 4) ? (__builtin_constant_p (hash->buckets[hi].string) && ((size_t)(const void *)((hash->buckets[hi].string) + 1) - (size_t)(const void *)(hash->buckets[hi].string) == 1) ? __builtin_strcmp (hash->buckets[hi].string, strings[i]) : (__extension__ ({ __const unsigned char *__s1 = (__const unsigned char *) (__const char *) (hash->buckets[hi].string); register int __result = __s1[0] - ((__const unsigned char *) (__const char *) (strings[i]))[0]; if (__s2_len > 0 && __result == 0) { __result = (__s1[1] - ((__const unsigned char *) (__const char *) (strings[i]))[1]); if (__s2_len > 1 && __result == 0) { __result = (__s1[2] - ((__const unsigned char *) (__const char *) (strings[i]))[2]); if (__s2_len > 2 && __result == 0) __result = (__s1[3] - ((__const unsigned char *) (__const char *) (strings[i]))[3]); } } __result; }))) : __builtin_strcmp (hash->buckets[hi].string, strings[i])))); }) == 0Constraint characters in unique sequence %d replaced with gap:strlen(constraintSeq) == nConstraintsWarning: ignoring constraints for %s: %s Another sequence has the same sequence but different constraints Sequence %s from constraints file is not in the alignment alnToUniq[last] >= 0 && alnToUniq[last] < nUniqueSeqWrong number of sequences: expected %d Empty header line followed by EOF Wrong name in phylip line %s Expected %s Read iSeq %d name %s seqsofar %s Too many characters (expected %d) for sequence named %s So far have: %s Warning! Found "." character(s). These are treated as gaps out-seqs[nSeq-1] == nKeep + nOldWrong number of characters for %s: expected %d but have %d instead. This sequence may be truncated, or another sequence may be too long. No empty line between sequence blocks (is the sequence count wrong?) No sequence data for last entry %s node>=0 && node < NJ->maxnodesfirst >= 0 && first < unique->nSeqonedimenmin lo %.4f guess %.4f hi %.4f range %.4f %.4f onedimenmin reaches optimum f(%.4f) = %.4f f2x %.4f Optimize alpha round %d to %.3f lk %.3f Optimize mult round %d to %.3f lk %.3f Optimizing alpha & mult converged Gamma(%d) LogLk = %.3f alpha = %.3f rescaling lengths by %.3f Gamma%dLogLk %.3f Approximate Alpha %.3f Rescale %.3f Optimizing alpha, starting at loglk %.3f rates != ((void *)0) && rates->nRateCategories > 0qo->pair1 != ((void *)0) && qo->pair2 != ((void *)0)iNode>=0 && (NJ->parent == ((void *)0) || NJ->parent[iNode]<0)OutDist for Node %d %f truth %f profiled %f truth %f pd_err %f NewOutDist for %d %f from dist %f selfd %f diam %f totdiam %f newActive %d Set Criterion to join %d %d with nActive=%d dist+penalty %.3f criterion %.3f NJ->nOutDistActive[join->j] >= nActiveNJ->nOutDistActive[join->i] >= nActivetop-hit search: nActive %d nVisible %d considering up to %d items iNode >= 0 && NJ->parent[iNode] < 0 && iNode != iInTopVisible replace %d=>%d with %d=>%d hit->j >= 0 && NJ->parent[hit->j] < 0iNodeBestCandidate >= 0 && NJ->parent[iNodeBestCandidate] < 0Resetting the top-visible list at nActive=%d Expanding visible set by walking up to active nodes at nActive=%d Top-visible list size %d (nActive %d m %d) join->i >= 0 && NJ->parent[join->i] < 0newj >= 0 && newj < NJ->maxnodes && newj != iNode && NJ->parent[newj] < 0join->j >= 0 && NJ->parent[join->j] < 0Top hits for %d from combined %d nActive=%d tophitsage %d %s Top hits for %d from children and source %d's %d hits, nUnique %d New top-hit list for %d profile-ops %ld (out-ops %ld): source %d age %d members Top hits for %d by refresh (%d unique age %d) nActive=%d lChild[i]->hits != ((void *)0) && lChild[i]->nHits > 0NJ->child[newnode].nChild == 2Top hits for %6d of %6d seqs (at seed %6d)Checking top hits for %6d of %6d seqsDistance limit for close neighbors %f weight %f ungapped %d Near neighbor %d (rank %d weight %f ungapped %d %d) #Close neighbors among leaves: 1st-level %ld 2nd-level %ld seeds %ld Worsen constraint: from %.3f to %.3f distance %.3f to %.3f: NNI scores ABvsCD %.5f ACvsBD %.5f ADvsBC %.5f choice %s Replaced weight %f with %f from w1 %f w2 %f PSame %f %f f12code %f f12other %f At %d: LogLk(%d:%.4f,%d:%.4f) = %.3f At root %d: LogLk((%d/%d),%d:%.3f) = %.3f Site likelihoods with rate category %d of %dRate %.3f Loglk %.3f SiteLogLkSwitched to using %d rate categories (CAT approximation) Rate categories were divided by %.3f so that average rate = 1.0 CAT-based log-likelihoods may not be comparable across runs Use -gamma for approximate but comparable Gamma(20) log-likelihoods Selected rate category %d rate %.3f for position %d GTR LogLk(%.5f %.5f %.5f %.5f %.5f %.5f) = %f gtr->iRate >= 0 && gtr->iRate < 6Optimize loglk from %.5f to %.5f eval %d lengths from %.5f %.5f %.5f %.5f %.5f to %.5f %.5f %.5f %.5f %.5f site_likelihoods == ((void *)0)Optimized quartet for %d rounds: ABvsCD %.5f ACvsBD %.5f ADvsBC %.5f Updating out-profile position %d weight %f (mult %f) Updated out-profile position %d weight %f (mult %f)out->codes[i] == 127 && fOut != ((void *)0)iFreqIn == profiles[in]->nVectorsIgnored unknown character %c (seen %lu times) WARNING! ONLY %.1f%% NUCLEOTIDE CHARACTERS -- IS THIS REALLY A NUCLEOTIDE ALIGNMENT? WARNING! %.1f%% NUCLEOTIDE CHARACTERS -- IS THIS REALLY A PROTEIN ALIGNMENT? Average profiles: pos %d in-w1 %f in-w2 %f bionjWeight %f to weight %f code %d outnode != NJ->root && outnode >= NJ->nSequpProfiles[outnode] != ((void *)0)Computing UpProfile for node %d with lenC %.4f lenD %.4f pair-loglk %.3f Compute upprofile of %d from %d and parents (vs. children %d %d) with weight %.3f Violate constraints %d distance_advantage %.3f constraint_penalty %.3f (children %d %d):Violate constraint %d at %d (children %d %d) penalties %.3f %.3f %.3f %d/%d %d/%d %d/%d %d/%d Testing Split around %d: A=%d B=%d C=%d D=up(%d) or node parent %d ML split tests for %6d of %6d internal splitsLocal bootstrap for %6d of %6d internal splitsRecompute %d from %d %d lengths %.4f %.4f Recompute %d from %d %d weight %.3f step->nodes[i] >= 0 && step->nodes[i] < NJ->maxnodesNJ->parent[parents[1]] == parents[0]SPR chain step %d for %d around %d swap %d %d deltaLen %.5f newAround[0] == nodeAround || newAround[1] == nodeAroundBeginning round %d of NNIs with ml? %d %s NNI round %%d of %%d, %%d of %%d splitsStarting quartet likelihood %.3f len %.3f %.3f %.3f %.3f %.3f NNI around %d: Swap A=%d B=%d C=%d D=out(C) -- choose %s %s %.4f Considering NNI around %d: Swap A=%d B=%d C=%d D=up(%d) or parent %d Skipping subtree at %d: child %d %d parent %d age %d subtreeAge %d support %.3f N up profiles at end of NNI: %d Optimize length for %d to %.3f Optimizing GTR model, step %d of %dGTRRates %.4f %.4f %.4f %.4f %.4f %.4f GTR Frequencies: %.4f %.4f %.4f %.4f GTR rates(ac ag at cg ct gt) %.4f %.4f %.4f %.4f %.4f %.4f NJ->profiles[c->child[0]] != ((void *)0)NJ->profiles[c->child[1]] != ((void *)0)SPR round %3d of %3d, %d of %d nodesSPR %s %d around %d chainLength %d of %d deltaLength %.5f swaps:Total branch-length is now %.4f was %.4f expected %.4f Warning while parsing tree: non-numeric label %s for internal node Added internal child %d of %d, stack size increase to %d not recognized as a branch lengthUp to nUp=%d stack size %d at %d Map %d to %d (parent %d nchild %d) c->child[j] >= 0 && c->child[j] < NJ->maxnode && NJ->parent[c->child[j]] == iAlignment sequence %d (unique %d) absent from input tree The starting tree (the argument to -intree) must include all sequences in the alignment! child >= 0 && child < maxnodeschildren[node].child[i] >= 0 && children[node].child[i] < maxnodesnode == root || children[node].nChild > 1Simplfied node %d has parent %d nchild %d Too few leaves, turning off top-hits Join %d %d %.6f lambda %.6f selfw %.3f %.3f new %d Constraint violation during neighbor-joining %d %d into %d penalty %.3f Constraint %d piece %d %d/%d %d/%d %d/%d Visible %d reset from %d to %d (%f vs. %f) deltaProfileVar actual %.6f estimated %.6f lambda actual %.3f estimated %.3f Roundoff error in outprofile@end: WeightError %f FreqError %f dVarO %f dVarDiam %f varIJ %f from dist %f weight %f (pos %d) bionjWeight %f %f NJ->nOutDistActive[join.i] == nActiveNJ->nOutDistActive[join.j] == nActiveRead %d sequences, %d positions Warning: logdist is now on by default and obsolete FastTree Version %s %s%s Alignment: %s %s distances: %s Joins: %s Support: %s CAT approximation with %d rate categoriesWarning: constraints file with less than 4 sequences ignored: alignment #%d in %s read %s seqs %d (%d unique) positions %d nameLast %s seqLast %s Refining topology: %d rounds ME-NNIs, %d rounds ME-SPRs, %d rounds ML-NNIs Total branch-length %.3f after %.2f sec Min_evolution NNIs converged at round %d -- skipping some rounds Search: %s%s %s %s %s TopHits: %s Pseudocount weight for comparing sequences with little overlap: %.3lf No rate variation across sitesGTR frequencies(A C G T) %.4f %.4f %.4f %.4f Total time: %.2f seconds Unique: %d/%d Bad splits: %d/%dViolating constraints: %d both bad: %d Worst delta-%s due to constraints: %.3fDist/N**2: by-profile %.3f (out %.3f) by-leaf %.3f avg-prof %.3f Top hits: close neighbors %ld/%d 2nd-level %ld refreshes %ldNNI: %ld SPR: %ld ML-NNI: %ld Max-lk operations: lk %ld posterior %ld approximate-posteriors %.2f%% Hill-climb: %ld Update-best: %ld %.2f*sqrtN close=%s refresh=%.2fTreeLogLk ML_NNI%d %.4lf MaxChange %.4lf Turning off heuristics for final round of ML NNIs%s ML-NNI round %d: LogLk %s= %.3f NNIs %d max delta %.2f Time %.2f%s Non-unique name '%s' in the alignment Initial topology in %.2f seconds TreeLogLk Length%d %.4lf MaxChange %.4lf %d rounds ML lengths: LogLk %s= %.3lf Max-change %.4lf%s Time %.2f Cannot use both -matrix and -nomatrix arguments!Usage for FastTree version %s %s%s: %sCannot be both slow and fastest Optimize all lengths: LogLk %s= %.3f Time %.2f -n argument for #input alignments must be > 0 not %s -refresh argument must be between 0 and 1 Cannot use -refresh unless -top is set above 0 -close argument must be between 0 and 1 Cannot use -close unless -top is set above 0 Detailed usage for FastTree %s %s%s: %s-exactml is not required -- exact posteriors is the default now Illlegal argument to -ncat (must be greater than zero): %s Illegal argument to -constraintWeight 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