├── .gitignore ├── INSTALL ├── LICENSE ├── Makefile.in ├── README ├── acinclude.m4 ├── aclocal.m4 ├── bin └── .gitignore ├── configure ├── configure.in ├── data ├── handalign │ ├── hidden.hsm │ ├── hiv_gp120 │ │ └── gp120.fa │ ├── jc.hsm │ ├── kimura.hsm │ ├── prot.hsm │ ├── prot1.hsm │ ├── prot2.hsm │ ├── prot3.hsm │ ├── prot4.hsm │ ├── tcod.eg │ └── tcod.hsm ├── hsmem │ ├── HSM1 │ ├── HSM2 │ ├── HSM3 │ └── HSM4 ├── phylocomposer │ ├── Makefile │ ├── counts.sxpr │ ├── fully_constrained.sxpr │ ├── geometric_parent.sxpr │ ├── gotoh_counts.sxpr │ ├── gotoh_node.sxpr │ ├── mixture_geometric_parent.sxpr │ ├── noseq.sxpr │ ├── postprof.sxpr │ ├── seq.sxpr │ ├── short.pl │ ├── short.sxpr │ ├── tkf91.sxpr │ ├── tkf91_aunt.sxpr │ ├── tkf91_aunt_with_emit_labels.sxpr │ ├── tkf91_node.sxpr │ ├── tkf91_node_with_emit_labels.sxpr │ ├── tkf91_parent.sxpr │ └── tkf91_serial.sxpr ├── stemloc │ ├── z1i2.tg │ ├── z2i2.tg │ ├── z3i2.tg │ └── z4i2.tg ├── tkfalign │ ├── phe.dist │ ├── phe.tree │ └── phe.trna ├── xrate │ ├── Lysine.stock │ └── Purine.stock ├── z1i2.tg ├── z2i2.tg ├── z3i2.tg └── z4i2.tg ├── doc ├── BuildingDart.txt ├── DART.txt ├── DartLogging.txt ├── DartPerlScripts.txt ├── DartPython.txt ├── DownloadingDart.txt ├── EvolDoer.txt ├── EvolSayer.txt ├── FastaFormat.txt ├── HandAlign.txt ├── HowMuchTrainingDataDoINeed.txt ├── IndieGram.txt ├── NewickFormat.txt ├── PhyloComposer.txt ├── StemLoc.txt ├── StockholmFormat.txt ├── XRateSoftware.txt ├── XrateFormat.txt ├── XrateGrammars.txt ├── XrateMacros.txt ├── XrateTutorial.txt └── index.html ├── grammars ├── 2rate_hky85.eg ├── README ├── XDecoder.eg ├── akaksgc.eg ├── ancestral_codon_bias.eg ├── ancestral_gc.eg ├── ancestral_gc3.eg ├── autodiscgamma.eg ├── binary-dna-rich.eg ├── binary-dna.eg ├── codon.eg ├── conservation_phylohmm.eg ├── cpg-dinuc-r4p16.eg ├── cpg-gapped-dinuc-r8p25.eg ├── demaio-et-al-2013 │ ├── S1.eg │ ├── S2.eg │ └── S3.eg ├── dinuc.eg ├── dna_alphabet.eg ├── dna_symmetric_gapsub.eg ├── ecm-tokenized.eg ├── exon.eg ├── fels81.eg ├── generators │ ├── Makefile │ ├── akaksgc.pl │ ├── akaksgc.tmpl.eg │ ├── cat.pl │ ├── codeml.pl │ ├── codeml.tmpl.eg │ ├── dummy.stock │ ├── hky85.tmpl.eg │ ├── ka_ks.pl │ ├── noself.pl │ ├── phylohmmgenerator.pl │ ├── sn.pl │ ├── sn.stk │ └── sn.tmpl.eg ├── heger-ponting-holmes-2009 │ ├── codonML-transmembrane.eg │ └── codonML.eg ├── hky85.eg ├── irrev.eg ├── jukescantor-parametric.eg ├── jukescantor.eg ├── kimura2.eg ├── kosiol-holmes-goldman-2007 │ ├── ecm-rest.eg │ └── ecm-unrest.eg ├── loopstem.eg ├── ncRnaDualStrand.eg ├── nielsen-yang.eg ├── nullprot.eg ├── nullrna.eg ├── ny_phylohmm.eg ├── overprinter.eg ├── pfold-loopmodel.eg ├── pfold-mix80-param.eg ├── pfold-mix80.eg ├── pfold-stemmodel.eg ├── pfold.eg ├── prot3.eg ├── prot3gap.eg ├── prot4.eg ├── protein_alphabet.eg ├── rescaled_branch_phylohmm.eg ├── rev.eg ├── rfam.eg ├── rgene.eg ├── rna_alphabet.eg ├── rnadecoder.eg ├── simgenome-12fly-ncrna-pipeline.eg ├── simgenome-original.eg ├── simgenome.eg ├── site_specific.eg ├── site_specific_protein.eg ├── sn.eg ├── sqrt.eg └── template.eg ├── install-sh ├── misc ├── README └── stl_vector.h ├── perl ├── Bubbles.pm ├── ChainDat.pm ├── DartSexpr.pm ├── MCMCcluster.pl ├── Newick.pm ├── PhyloGram.pm ├── PhyloGram │ ├── Chain.pm │ ├── Dna.pm │ └── Protein.pm ├── Roc.pm ├── SequenceIterator.pm ├── Stockholm.pm ├── Stockholm │ └── Database.pm ├── ancrec_to_seq.pl ├── animate-evolsayer.pl ├── baliphy2stockholm.pl ├── calc_ss_cons.pl ├── clustal2stockholm.pl ├── col2stockholm.pl ├── colorstock.pl ├── compareParams.pl ├── constock.pl ├── copy2stderr.pl ├── copyparams.pl ├── dartlog.pl ├── drop-gappy-columns.pl ├── ecm2eg-tokenized.pl ├── ecm2eg.pl ├── evolsayer.pl ├── extract_ss.pl ├── fancyeisen.pl ├── fasta2stockholm.pl ├── foldplot.pl ├── homstrad2stockholm.pl ├── hsm2xgram.pl ├── hsmplot.pl ├── iteridem.pl ├── maf2stockholm.pl ├── majorcons.pl ├── msf2stockholm.pl ├── old_xrate.pl ├── optic2stockholm.pl ├── pandit2stockholm.pl ├── percentid.pl ├── phylodirector.pl ├── phylogramTool.pl ├── prank2stock.pl ├── protpaleo.pl ├── quick_fasta2stockholm.pl ├── quickgmix.pl ├── quickidrate.pl ├── rnafold2stockholm.pl ├── sanebp.pl ├── seqdotplot.pl ├── simgenome.pl ├── splitstock.pl ├── sscolor.pl ├── sscolorMult.pl ├── stkCompareAnnot.pl ├── stockfilm.pl ├── stockfootage.pl ├── stockholm2ct.pl ├── stockholm2fasta.pl ├── stockholm2mpd.pl ├── stocktree.pl ├── testharness.pl ├── toParams.pl ├── tokenize.pl ├── trimstock.pl ├── unalign.pl ├── visualizeRates.pl ├── vslice.pl ├── windowlicker.pl ├── xgram2hsm.pl └── xratecgi.pl ├── python ├── .cvsignore ├── .project ├── .pydevproject ├── .settings │ └── org.eclipse.ltk.core.refactoring.prefs ├── README ├── SExpr.py ├── XGram │ ├── Exceptions.py │ ├── Generator │ │ ├── GeneratorAlphabets.py │ │ ├── GeneratorChainComponent.py │ │ ├── GeneratorChains.py │ │ ├── GeneratorExpressions.py │ │ ├── GeneratorGrammars.py │ │ ├── GeneratorInitialStates.py │ │ ├── GeneratorRates.py │ │ ├── GeneratorTransitions.py │ │ ├── Prebuilt │ │ │ ├── Codons.py │ │ │ ├── DNA.py │ │ │ ├── ProteinFamily.py │ │ │ ├── ProteinSites.py │ │ │ ├── RNA.py │ │ │ └── __init__.py │ │ └── __init__.py │ ├── Lexer.py │ ├── Model │ │ ├── ModelAlphabet.py │ │ ├── ModelAnnotation.py │ │ ├── ModelChain.py │ │ ├── ModelGrammar.py │ │ ├── ModelModel.py │ │ ├── ModelParameter.py │ │ ├── ModelProbabilisticModel.py │ │ ├── ModelRule.py │ │ └── __init__.py │ ├── Parser.py │ ├── Run │ │ ├── RunIteration.py │ │ └── __init__.py │ ├── Tests │ │ ├── .cvsignore │ │ ├── GeneratorCodonsTest.py │ │ ├── GeneratorDNATest.py │ │ ├── GrammarTest.py │ │ └── ParserTest.py │ ├── Utils │ │ ├── Stk.py │ │ ├── UtilsMali.py │ │ ├── __init__.py │ │ └── utilGen.py │ ├── XGram.py │ ├── __init__.py │ ├── data │ │ ├── akaksgc.eg │ │ ├── ancestral_gc.eg │ │ ├── ancestral_gc_trained.eg │ │ ├── cluster_5750.stk │ │ ├── codons_blocks3.eg │ │ ├── dpse_dmel.stk │ │ ├── evolutionary_trace.eg │ │ ├── hky85.eg │ │ ├── kimura2.eg │ │ ├── ncrna.FBtr0081064.stk │ │ ├── nullprot.eg │ │ ├── nullrna.eg │ │ ├── pf00017.stk │ │ ├── pf00017_truncated.stk │ │ ├── pf00017_withtree.stk │ │ ├── pfold.eg │ │ ├── rf00001.stk │ │ ├── rf00013.stk │ │ ├── rf00013_withtree.stk │ │ ├── rf00503.stk │ │ └── sn.eg │ ├── parsetab.py │ └── test │ │ ├── codonml.py │ │ ├── dna.py │ │ ├── evolutionary_trace.py │ │ ├── get_grammar.py │ │ ├── kimura2.py │ │ ├── parser.out │ │ ├── parser.py │ │ ├── parsetab.py │ │ ├── pfold.py │ │ ├── protein_family.py │ │ ├── rna.py │ │ └── rna_iterations.py ├── extra_functions.py ├── mixture_gen.py ├── parseSexpr.py ├── parsetab.py ├── setup.py └── visualizeReconstruction.py ├── scheme ├── t │ ├── ny.eg │ ├── ny2.eg │ └── xrate-stdlib.test.scm └── xrate-stdlib.scm ├── src ├── .gitignore ├── Weighbor │ ├── COPYRIGHT │ ├── Doc │ │ ├── weighbor.man │ │ ├── weighbor.ps │ │ └── weighbor.txt │ ├── INSTALL │ ├── Makefile.in │ ├── README │ ├── build.c │ ├── calcb.c │ ├── calcq.c │ ├── calcz.c │ ├── calerf.c │ ├── cnoweb.tex │ ├── io.c │ ├── io.h │ ├── matrix.c │ ├── matrix.h │ ├── noise.c │ ├── tree.c │ ├── tree.eps │ ├── tree.h │ ├── weighbor.c │ └── weighbor.h ├── amap │ ├── FileBuffer.h │ ├── Makefile.in │ ├── MultiSequence.h │ ├── MultiSequenceDag.h │ ├── SafeVector.h │ ├── Sequence.h │ ├── SparseMatrix.h │ ├── amap_adapter.cc │ ├── amap_adapter.h │ ├── dotplot.cc │ └── dotplot.h ├── beagle │ ├── Makefile │ └── xrate-beagle.cc ├── config.h.in ├── ecfg │ ├── A1pp.pep │ ├── Makefile.in │ ├── ecfg.cc │ ├── ecfg.h │ ├── ecfg_branch_length_em.cc │ ├── ecfg_branch_length_em.h │ ├── ecfgdp.cc │ ├── ecfgdp.h │ ├── ecfgenv.cc │ ├── ecfgenv.h │ ├── ecfgkeywords.h │ ├── ecfgmain.cc │ ├── ecfgmain.h │ ├── ecfgplacer.cc │ ├── ecfgplacer.h │ ├── ecfgsexpr.cc │ ├── ecfgsexpr.h │ ├── fastprune.cc │ ├── fastprune.h │ ├── guile-ecfg.cc │ ├── guile-ecfg.h │ ├── hsm2eg.cc │ ├── paircfg_xfold.cc │ ├── paircfg_xfold.h │ ├── pfold.cc │ ├── pfold.h │ ├── protgrammar.cc │ ├── protgrammar.h │ ├── simgram.cc │ ├── single_chain_ecfg.cc │ ├── single_chain_ecfg.h │ ├── t │ │ ├── 00_bad_expr.fail │ │ ├── 01_not_atom.fail │ │ ├── Makefile │ │ ├── No_substitution_information.stockholm │ │ ├── No_substitution_information.xrange │ │ ├── README │ │ ├── Reversible_acgt_cycler.stockholm │ │ ├── Reversible_acgt_cycler.xrange │ │ ├── Reversible_acgt_cycler_low_seed.stockholm │ │ ├── Reversible_acgt_cycler_low_seed.xrange │ │ ├── Short-Purine.mul │ │ ├── Unidirectional_acgt_cycler.stockholm │ │ ├── Unidirectional_acgt_cycler.xrange │ │ ├── badgram.pl │ │ ├── bigtree.nh │ │ ├── bp.stk │ │ ├── bug1.README │ │ ├── bug1.eg │ │ ├── bug1.stock │ │ ├── dinuc.stk │ │ ├── dualstrand.stk │ │ ├── dummy.stock │ │ ├── hybrid.eg │ │ ├── hybrid.stock │ │ ├── invrep.stk │ │ ├── low_seed.xrate │ │ ├── low_seed_irrev.xrate │ │ ├── newexample.eg │ │ ├── notree.stk │ │ ├── sane.stk │ │ ├── sim1.eg │ │ ├── sim1.tree1.nh │ │ ├── sim1.tree2.nh │ │ ├── simtest.pl │ │ ├── sn.eg │ │ ├── sn.meta.eg │ │ ├── sn.tree1.nh │ │ ├── sn.tree2.nh │ │ ├── testxrate.pl │ │ ├── tiny.stk │ │ └── tree.nh │ ├── testchain.cc │ ├── testsexpr.cc │ └── xrate.cc ├── evoldoer │ ├── Makefile.in │ ├── evoldoer.cc │ ├── t │ │ ├── 3way.nh │ │ └── longz.nh │ ├── tkfstparams.pl │ ├── tkfstructuretree.cc │ └── tkfstructuretree.h ├── guile │ ├── Makefile.in │ ├── assmap.cc │ ├── assmap.h │ ├── darts.cc │ ├── dpm-type.h │ ├── guile-keywords.h │ ├── guile-newick-keywords.h │ ├── guile-stockholm-keywords.h │ ├── guile-xrate-keywords.h │ ├── newick-type.cc │ ├── newick-type.h │ ├── perl │ │ └── obo2schelog.pl │ ├── scm │ │ ├── goslim.scm │ │ └── schelog.scm │ ├── stockholm-type.cc │ ├── stockholm-type.h │ └── t │ │ ├── test.scm │ │ ├── test2.scm │ │ ├── test3.scm │ │ ├── test4.scm │ │ └── tiny.stk ├── handel │ ├── Makefile.in │ ├── README │ ├── TODO │ ├── alitrans.cc │ ├── alitrans.h │ ├── consdp.cc │ ├── consdp.h │ ├── ehmm.cc │ ├── ehmm.h │ ├── handalign.cc │ ├── handelbase.cc │ ├── handelbase.h │ ├── hmmoc_adapter.cc │ ├── hmmoc_adapter.h │ ├── hmmoc_adapter_opts.cc │ ├── hmmoc_adapter_opts.h │ ├── hmmoc_banding.h │ ├── initalign.cc │ ├── initalign.h │ ├── inline_ehmm.h │ ├── movement.cc │ ├── movement.h │ ├── multiwaydp.cc │ ├── multiwaydp.h │ ├── phylocomposer.cc │ ├── posthand.cc │ ├── recorder.cc │ ├── recorder.h │ ├── rivas.cc │ ├── rivas.h │ ├── simpleehmm.cc │ ├── simpleehmm.h │ ├── t │ │ ├── COX2.fasta │ │ ├── COX2.stock │ │ ├── README │ │ ├── U30.newick │ │ ├── hidden.hsm │ │ ├── jc.hsm │ │ ├── prot.hsm │ │ ├── short.stk │ │ ├── simband.pl │ │ ├── tc1.stk │ │ ├── testehmm.cc │ │ ├── tiny.stk │ │ └── transducer.sexpr │ ├── talike.cc │ ├── talike.h │ ├── tkftrans.cc │ ├── tkftrans.h │ ├── transducer.cc │ ├── transducer.h │ ├── transducer_keywords.h │ ├── transducer_sexpr.cc │ ├── transducer_sexpr.h │ ├── treeshuffler.cc │ └── treeshuffler.h ├── hmm │ ├── Makefile.in │ ├── fastgibbs.cc │ ├── fastgibbs.h │ ├── gibbshmm.cc │ ├── inline_transmat.h │ ├── pairenv.cc │ ├── pairenv.h │ ├── pairhmm.cc │ ├── pairhmm.h │ ├── pairhmmem.cc │ ├── pairhmmem.h │ ├── pairphmm.cc │ ├── pairphmm.h │ ├── postpairhmm.cc │ ├── postpairhmm.h │ ├── singlealign.cc │ ├── singlealign.h │ ├── singledp.cc │ ├── singledp.h │ ├── singledptmpl.cc │ ├── singledptmpl.h │ ├── singlefastdp.cc │ ├── singlefastdp.h │ ├── singlehmm.h │ ├── singlephmm.cc │ ├── singlephmm.h │ ├── singletmpl.cc │ ├── singletmpl.h │ ├── testhmm.cc │ ├── transmat.cc │ └── transmat.h ├── hsm │ ├── 1433.mul │ ├── DBrooks-trial3 │ ├── DBrooks-trial4 │ ├── HSM │ ├── Makefile.dart-hsm │ ├── Makefile.in │ ├── Test2Table.pl │ ├── TestRND │ ├── TestRND.results │ ├── alignstrip.pl │ ├── branch_length_em.cc │ ├── branch_length_em.h │ ├── crapfilter.pl │ ├── em_matrix.cc │ ├── em_matrix.h │ ├── em_matrix_base.cc │ ├── em_matrix_base.h │ ├── hsmloglike.pl │ ├── indexer.pl │ ├── make_figs │ ├── makepfamdirs.pl │ ├── newtonraphson.cc │ ├── newtonraphson.h │ ├── phatrates.pl │ ├── phylo_em.h │ ├── plotrates.pl │ ├── rind_em_matrix.cc │ ├── rind_em_matrix.h │ ├── showcounts.pl │ ├── showrates.pl │ ├── smdist.cc │ ├── smdist.h │ ├── t │ │ ├── mytest.c │ │ ├── mytest2.pl │ │ ├── testemmatrix.cc │ │ ├── testemmatrix.mul │ │ ├── testemmatrix.mws │ │ ├── testemmatrix.phylip │ │ ├── testemmatrix2.mws │ │ ├── testnewtonraphson.cc │ │ └── testnewtonraphson.mws │ ├── top100 │ ├── weighpfam.pl │ ├── zf.dist │ ├── zf.index │ ├── zf.mul │ └── zf.tree ├── indiegram │ ├── Makefile.in │ ├── README │ ├── igdefaults.cc │ ├── igdefaults.h │ ├── igloopmodel.eg │ ├── igmain.cc │ ├── igmain.h │ ├── igstemmodel.eg │ ├── indiegram.cc │ ├── perl │ │ ├── ComposedTreeTransducer.pm │ │ ├── ComposedTreeTransducer │ │ │ ├── FourWayComposedTT.pm │ │ │ └── TripletSCFG.pm │ │ ├── TreeTransducer.pm │ │ ├── TreeTransducer │ │ │ ├── BranchTT.pm │ │ │ └── SingletTT.pm │ │ ├── Util.pm │ │ ├── compareTM.pl │ │ ├── fourWay.pl │ │ ├── generateIndiegramStuff.pl │ │ ├── testComposition.pl │ │ └── tripletSCFG.pl │ ├── postprobs.cc │ ├── postprobs.h │ ├── statesorter.cc │ ├── statesorter.h │ ├── t │ │ ├── Y.stk │ │ ├── g2intron.aln1.aligned.stk │ │ ├── g2intron.aln1.stk │ │ ├── nanos.aligned.stk │ │ ├── nanos.stk │ │ ├── tRNA.aln1.aligned.stk │ │ ├── tRNA.aln1.stk │ │ ├── tiny.stk │ │ ├── tinytiny.stk │ │ └── trivial.stk │ ├── testtkfst.cc │ ├── testtripletscfg.cc │ ├── testtripletscfgdp.cc │ ├── tkfst.cc │ ├── tkfst.cc.empty │ ├── tkfst.h │ ├── tripletscfg.cc │ ├── tripletscfg.h │ ├── tripletscfgdp.cc │ ├── tripletscfgdp.h │ └── tt │ │ ├── README │ │ ├── bifurcTest.branch.tt │ │ ├── bifurcTest.singlet.tt │ │ ├── bifurcTest.valid.fullyreduced.tm │ │ ├── bifurcTest.valid.reduced.tm │ │ ├── bifurcTest.valid.tm │ │ ├── redundantTest.branch.tt │ │ ├── redundantTest.singlet.tt │ │ ├── simpleTest.branch.tt │ │ ├── simpleTest.singlet.tt │ │ ├── simpleTest.valid.fullyreduced.tm │ │ ├── simpleTest.valid.reduced.tm │ │ ├── simpleTest.valid.tm │ │ ├── template.tt │ │ ├── tkfst.branch.tt │ │ ├── tkfst.fullyreduced.tm │ │ ├── tkfst.reduced.tm │ │ ├── tkfst.singlet.tt │ │ ├── tkfst.tm │ │ ├── tkfst.tripletSCFG │ │ ├── tkfst.valid.fullyreduced.tm │ │ ├── tkfst.valid.reduced.tm │ │ └── tkfst.valid.tm ├── irrev │ ├── Makefile.in │ ├── irrev_em_matrix.cc │ ├── irrev_em_matrix.h │ ├── irrev_xrate.cc │ ├── pfunc_em_matrix.h │ ├── t │ │ ├── HSM1 │ │ ├── HSM2 │ │ ├── No_substitution_information.stockholm │ │ ├── No_substitution_information.xrange │ │ ├── README │ │ ├── Reversible_acgt_cycler.stockholm │ │ ├── Reversible_acgt_cycler.xrange │ │ ├── Reversible_acgt_cycler_low_s.xrate │ │ ├── Reversible_acgt_cycler_low_seed.stockholm │ │ ├── Reversible_acgt_cycler_low_seed.xrange │ │ ├── Reversible_acgt_cycler_low_seed.xrate │ │ ├── SansonEtAl.xrate │ │ ├── Unidirectional_acgt_cyc.xrate │ │ ├── Unidirectional_acgt_cycler.stockholm │ │ ├── Unidirectional_acgt_cycler.xrange │ │ ├── Unidirectional_acgt_cycler.xrate │ │ ├── exphsm.cc │ │ ├── four_column_unid_acgt_cycler.stockholm │ │ ├── four_column_unid_acgt_cycler.xrange │ │ ├── irrev_exphsm.cc │ │ ├── low_seed.xrate │ │ ├── perl │ │ │ └── sansonetal.pl │ │ ├── test_exphsm.in │ │ ├── test_exphsm.pl │ │ └── test_irrev_xrate.pl │ └── xsim.cc ├── make.common.in ├── make.defs.in ├── newmat │ ├── Makefile.in │ ├── bandmat.cc │ ├── boolean.h │ ├── cholesky.cc │ ├── controlw.h │ ├── evalue.cc │ ├── example.cc │ ├── fft.cc │ ├── garch.cc │ ├── hholder.cc │ ├── include.h │ ├── jacobi.cc │ ├── linalg.cc │ ├── linalg.h │ ├── myexcept.cc │ ├── myexcept.h │ ├── newfft.cc │ ├── newmat.h │ ├── newmat1.cc │ ├── newmat2.cc │ ├── newmat3.cc │ ├── newmat4.cc │ ├── newmat5.cc │ ├── newmat6.cc │ ├── newmat7.cc │ ├── newmat8.cc │ ├── newmat9.cc │ ├── newmatap.h │ ├── newmatex.cc │ ├── newmatio.h │ ├── newmatnl.cc │ ├── newmatnl.h │ ├── newmatrc.h │ ├── newmatrm.cc │ ├── newmatrm.h │ ├── nl_ex.cc │ ├── nm_ex1.cc │ ├── nm_ex2.cc │ ├── nm_exp.cc │ ├── nm_exp.h │ ├── precisio.h │ ├── sl_ex.cc │ ├── solution.cc │ ├── solution.h │ ├── sort.cc │ ├── submat.cc │ ├── svd.cc │ ├── test_exc.cc │ ├── tmt.cc │ ├── tmt.h │ ├── tmt1.cc │ ├── tmt2.cc │ ├── tmt3.cc │ ├── tmt4.cc │ ├── tmt5.cc │ ├── tmt6.cc │ ├── tmt7.cc │ ├── tmt8.cc │ ├── tmt9.cc │ ├── tmta.cc │ ├── tmtb.cc │ ├── tmtc.cc │ ├── tmtd.cc │ ├── tmte.cc │ ├── tmtf.cc │ ├── tmtg.cc │ ├── tmth.cc │ ├── tmti.cc │ ├── tmtj.cc │ ├── tmtk.cc │ ├── tmtl.cc │ └── tmtm.cc ├── ontology │ ├── Makefile.in │ ├── onto_keywords.h │ ├── onto_sexpr.cc │ ├── onto_sexpr.h │ ├── t │ │ ├── error1.tsm │ │ ├── test1.tsm │ │ ├── test2.tsm │ │ ├── test3.tsm │ │ ├── test4.tsm │ │ ├── test5.eg │ │ ├── test5.stk │ │ ├── test5.tsm │ │ └── test6.tsm │ └── termx.cc ├── protpal │ ├── AlignmentEnvelope.cc │ ├── AlignmentEnvelope.h │ ├── AlignmentSampler.cc │ ├── AlignmentSampler.h │ ├── ImportExport.cc │ ├── ImportExport.h │ ├── Makefile.in │ ├── MePal.cc │ ├── MyMap.h │ ├── Placement.cc │ ├── Placement.h │ ├── Q.cc │ ├── Q.h │ ├── ReadProfileScore.cc │ ├── ReadProfileScore.h │ ├── algebras.cc │ ├── algebras.h │ ├── exactMatch.cc │ ├── exactMatch.h │ ├── json.cc │ ├── json.h │ ├── profile.cc │ ├── profile.h │ ├── protpal.cc │ ├── reconstruction.cc │ ├── reconstruction.h │ ├── testing │ │ ├── testSeqs.stk │ │ └── testTree.newick │ ├── transducer.cc │ ├── transducer.h │ ├── utils.cc │ └── utils.h ├── psw │ ├── Makefile.in │ ├── dpswalign.cc │ ├── dpswtrain.cc │ ├── lufcy-momba.fa │ ├── nwalign.cc │ ├── ppswalign.cc │ ├── ppswtrain.cc │ ├── pswmain.cc │ ├── pswmain.h │ ├── pswmodel.cc │ ├── pswmodel.h │ ├── simplepsw.cc │ ├── simplepsw.h │ └── swalign.cc ├── randlib │ ├── Makefile.in │ ├── com.cc │ ├── doc │ │ ├── Basegen.c.doc │ │ ├── HOWTOGET │ │ ├── README │ │ ├── randlib.c.chs │ │ └── randlib.c.fdoc │ ├── linpack.cc │ ├── randlib.cc │ └── randlib.h ├── scfg │ ├── Makefile.dart-scfg │ ├── Makefile.in │ ├── cfgdotplot.cc │ ├── cfgdotplot.h │ ├── cfgkeywords.h │ ├── cfgsexpr.cc │ ├── cfgsexpr.h │ ├── covmodel.cc │ ├── covmodel.h │ ├── foldenv.cc │ ├── foldenv.h │ ├── foldfile.cc │ ├── foldfile.h │ ├── makestack.pl │ ├── paircfg.cc │ ├── paircfg.h │ ├── paircfgdp.cc │ ├── paircfgdp.h │ ├── paircfgem.cc │ ├── paircfgem.h │ ├── pairpcfg.cc │ ├── pairpcfg.h │ ├── postenv.cc │ ├── postenv.h │ ├── subseqiter.h │ ├── testelim.cc │ ├── testfoldenv.cc │ ├── testpaircfg.cc │ ├── testpaircfgdp.cc │ ├── testsampletraceback.cc │ ├── wehits.cc │ └── wehits.h ├── seq │ ├── Makefile.in │ ├── aligncluster.cc │ ├── alignment.cc │ ├── alignment.h │ ├── biosequence.cc │ ├── biosequence.h │ ├── cmpalign.cc │ ├── cmpfold.cc │ ├── dirichlet.cc │ ├── dirichlet.h │ ├── distmat.cc │ ├── distmat.h │ ├── gff.cc │ ├── gff.h │ ├── local.cc │ ├── local.h │ ├── pfunc.cc │ ├── pfunc.h │ ├── pkeywords.h │ ├── psexpr.cc │ ├── psexpr.h │ ├── pvar.cc │ ├── pvar.h │ ├── seqlogo.cc │ ├── seqlogo.h │ ├── stockholm.cc │ ├── stockholm.h │ ├── suffix.cc │ ├── suffix.h │ ├── teststock.cc │ └── wordcount.cc ├── stemloc │ ├── B12.mul │ ├── B12.rna │ ├── KNOWN-BUGS │ ├── Makefile.in │ ├── Nanos-Drosophilae-virilis-melanogaster.aligned │ ├── Nanos-Drosophilae-virilis-melanogaster.fa │ ├── Nanos-Drosophilae-virilis-melanogaster.folded │ ├── TUTORIAL │ ├── Wishlist │ ├── alignparams.tg │ ├── cmpparams.tg │ ├── dynalign.trna │ ├── dynalign.trna.aligned │ ├── dynalign.trna.aligned.folded │ ├── elegans-histone-utrs.rna │ ├── foldparams.tg │ ├── gc2gr-ss.cc │ ├── k10-3utr.aligned │ ├── k10-3utr.dna │ ├── nanos-3utr.dna │ ├── nanos-tiny.rna │ ├── quickalign.cc │ ├── quickalign.h │ ├── quickstem.cc │ ├── quickstem.h │ ├── refloc.cc │ ├── savedefaults.cc │ ├── sldefaults.cc │ ├── sldefaults.h │ ├── slkeywords.h │ ├── slmain.cc │ ├── slmain.h │ ├── stemloc.cc │ ├── stempair.cc │ ├── stempair.h │ ├── superpair.cc │ ├── superpair.h │ ├── superstem.cc │ ├── superstem.h │ ├── tRNA.rna │ ├── tetrastem.cc │ ├── tetrastem.h │ └── tetris.cc ├── telegraph │ ├── Makefile.in │ ├── TGVAR-TEST │ ├── add_this_to_.emacs │ ├── bison-mode.el │ ├── dummy.tg │ ├── flex-mode.el │ ├── make-regexp.el │ ├── splice_site_example.tg │ ├── swexample.tg │ ├── testtgvar.cc │ ├── tgvar.cc │ ├── tgvar.h │ ├── tutorial.tex │ └── y.tab.h ├── tkf │ ├── Makefile.in │ ├── countblocks.cc │ ├── testtkfhmm.cc │ ├── tkf.mws │ ├── tkfalign.cc │ ├── tkfchildpairdp.cc │ ├── tkfchildpairdp.h │ ├── tkfcoeff.cc │ ├── tkfcoeff.h │ ├── tkfdata.cc │ ├── tkfdata.h │ ├── tkfdistance.cc │ ├── tkfdistmat.cc │ ├── tkfdistmat.h │ ├── tkfem.cc │ ├── tkfem.h │ ├── tkfemit.cc │ ├── tkfhmm.cc │ ├── tkfhmm.h │ ├── tkfidem.cc │ ├── tkfidmcmc.cc │ ├── tkfnodedp.cc │ ├── tkfnodedp.h │ ├── tkfopts.cc │ ├── tkfopts.h │ ├── tkfparams.cc │ ├── tkfparams.h │ ├── tkfsequence.cc │ └── tkfsequence.h ├── tree │ ├── Makefile.in │ ├── PAM100.internal │ ├── TestTree │ ├── diagonalised_matrix_factory.cc │ ├── diagonalised_matrix_factory.h │ ├── drawpstree.cc │ ├── eztree.cc │ ├── getinsertions.cc │ ├── getpam.cc │ ├── hasegawa.cc │ ├── hasegawa.h │ ├── irrev_diag_matrix_factory.cc │ ├── irrev_diag_matrix_factory.h │ ├── nj.cc │ ├── nj.h │ ├── pam.cc │ ├── pam.h │ ├── phylogeny.cc │ ├── phylogeny.h │ ├── ps_tree.cc │ ├── ps_tree.h │ ├── pstreealign.h │ ├── rate_matrix.cc │ ├── rate_matrix.h │ ├── reroot.cc │ ├── subdistmat.cc │ ├── subdistmat.h │ ├── substitution_matrix_factory.cc │ ├── substitution_matrix_factory.h │ ├── testpam.cc │ ├── testtree.cc │ ├── tree_alignment.cc │ └── tree_alignment.h └── util │ ├── Makefile.in │ ├── Regexp.cc │ ├── Regexp.h │ ├── array2d.h │ ├── checkderiv.h │ ├── chooser.h │ ├── counter.h │ ├── dartdebug.cc │ ├── dartdebug.h │ ├── dartmap.h │ ├── dexception.cc │ ├── dexception.h │ ├── discrete_gamma.cc │ ├── discrete_gamma.h │ ├── guile-defs.cc │ ├── guile-defs.h │ ├── guile-keywords.h │ ├── input_string.h │ ├── istream_get_iterator.h │ ├── logfile.cc │ ├── logfile.h │ ├── logprob.h │ ├── macros.h │ ├── make-logtags.pl │ ├── map_keys.h │ ├── math_fn.cc │ ├── math_fn.h │ ├── maximise.h │ ├── multi_array.h │ ├── newmat_adaptors.cc │ ├── newmat_adaptors.h │ ├── nstring.h │ ├── nullstream.cc 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