├── .gitattributes ├── LICENSE ├── README.md ├── SynGAP.environment.yaml ├── __pycache__ ├── custom.cpython-310.pyc ├── dual.cpython-310.pyc ├── dual.cpython-38.pyc ├── evi.cpython-310.pyc ├── eviplot.cpython-310.pyc ├── genepair.cpython-310.pyc └── triple.cpython-310.pyc ├── bin ├── CPC2_standalone-1.0.1 │ ├── .gitignore │ ├── LICENSE │ ├── README.md │ ├── bin │ │ ├── CPC2.py │ │ ├── compress.py │ │ └── seqio.py │ ├── data │ │ ├── cpc2.model │ │ ├── cpc2.range │ │ └── example.fa │ ├── example_output.txt │ └── libs │ │ └── libsvm │ │ ├── libsvm-3.18.tar.gz │ │ └── libsvm-3.18 │ │ ├── COPYRIGHT │ │ ├── FAQ.html │ │ ├── Makefile │ │ ├── Makefile.win │ │ ├── README │ │ ├── heart_scale │ │ ├── java │ │ ├── Makefile │ │ ├── libsvm.jar │ │ ├── libsvm │ │ │ ├── svm.java │ │ │ ├── svm.m4 │ │ │ ├── svm_model.java │ │ │ ├── svm_node.java │ │ │ ├── svm_parameter.java │ │ │ ├── svm_print_interface.java │ │ │ └── svm_problem.java │ │ ├── svm_predict.java │ │ ├── svm_scale.java │ │ ├── svm_toy.java │ │ ├── svm_train.java │ │ └── test_applet.html │ │ ├── matlab │ │ ├── Makefile │ │ ├── README │ │ ├── libsvmread.c │ │ ├── libsvmwrite.c │ │ ├── make.m │ │ ├── svm_model_matlab.c │ │ ├── svm_model_matlab.h │ │ ├── svmpredict.c │ │ └── svmtrain.c │ │ ├── python │ │ ├── Makefile │ │ ├── README │ │ ├── svm.py │ │ └── svmutil.py │ │ ├── svm-predict │ │ ├── svm-predict.c │ │ ├── svm-scale │ │ ├── svm-scale.c │ │ ├── svm-toy │ │ ├── gtk │ │ │ ├── Makefile │ │ │ ├── callbacks.cpp │ │ │ ├── callbacks.h │ │ │ ├── interface.c │ │ │ ├── interface.h │ │ │ ├── main.c │ │ │ └── svm-toy.glade │ │ ├── qt │ │ │ ├── Makefile │ │ │ └── svm-toy.cpp │ │ └── windows │ │ │ └── svm-toy.cpp │ │ ├── svm-train │ │ ├── svm-train.c │ │ ├── svm.cpp │ │ ├── svm.def │ │ ├── svm.h │ │ ├── svm.o │ │ ├── tools │ │ ├── README │ │ ├── checkdata.py │ │ ├── easy.py │ │ ├── grid.py │ │ └── subset.py │ │ └── windows │ │ ├── libsvm.dll │ │ ├── libsvmread.mexw64 │ │ ├── libsvmwrite.mexw64 │ │ ├── svm-predict.exe │ │ ├── svm-scale.exe │ │ ├── svm-toy.exe │ │ ├── svm-train.exe │ │ ├── svmpredict.mexw64 │ │ └── svmtrain.mexw64 ├── SwissProt │ ├── uniprot_sprot.fasta │ └── uniprot_sprot.fasta.dmnd ├── genBlast_v138_linux_x86_64 │ ├── alignscore.txt │ ├── bl2seq │ ├── blastall │ ├── blastclust │ ├── blastpgp │ ├── copymat │ ├── data │ │ ├── BLOSUM45 │ │ ├── BLOSUM62 │ │ ├── BLOSUM80 │ │ ├── KSat.flt │ │ ├── KSchoth.flt │ │ ├── KSgc.flt │ │ ├── KShopp.flt │ │ ├── KSkyte.flt │ │ ├── KSpcc.mat │ │ ├── KSpur.flt │ │ ├── KSpyr.flt │ │ ├── PAM30 │ │ ├── PAM70 │ │ ├── UniVec.nhr │ │ ├── UniVec.nin │ │ ├── UniVec.nsq │ │ ├── UniVec_Core.nhr │ │ ├── UniVec_Core.nin │ │ ├── UniVec_Core.nsq │ │ ├── asn2ff.prt │ │ ├── bstdt.val │ │ ├── ecnum_ambiguous.txt │ │ ├── ecnum_specific.txt │ │ ├── featdef.val │ │ ├── gc.val │ │ ├── humrep.fsa │ │ ├── lineages.txt │ │ ├── makerpt.prt │ │ ├── objprt.prt │ │ ├── pubkey.enc │ │ ├── seqcode.val │ │ ├── sequin.hlp │ │ ├── sgmlbb.ent │ │ └── taxlist.txt │ ├── fastacmd │ ├── formatdb │ ├── formatrpsdb │ ├── genblast_v138_linux_x86_64 │ ├── impala │ ├── makemat │ ├── megablast │ ├── rpsblast │ └── seedtop ├── iTAK │ ├── README.md │ ├── bin │ │ ├── hmmbuild │ │ ├── hmmpress │ │ ├── hmmscan │ │ └── itak.pm │ ├── bug │ ├── database │ │ ├── GA_table.txt │ │ ├── PK_class_desc.txt │ │ ├── Pkinase_sub_MAK.hmm │ │ ├── Pkinase_sub_MAK.hmm.h3f │ │ ├── Pkinase_sub_MAK.hmm.h3i │ │ ├── Pkinase_sub_MAK.hmm.h3m │ │ ├── Pkinase_sub_MAK.hmm.h3p │ │ ├── Pkinase_sub_WNK1.hmm │ │ ├── Pkinase_sub_WNK1.hmm.h3f │ │ ├── Pkinase_sub_WNK1.hmm.h3i │ │ ├── Pkinase_sub_WNK1.hmm.h3m │ │ ├── Pkinase_sub_WNK1.hmm.h3p │ │ ├── Plant_Pkinase_fam.hmm │ │ ├── Plant_Pkinase_fam.hmm.h3f │ │ ├── Plant_Pkinase_fam.hmm.h3i │ │ ├── Plant_Pkinase_fam.hmm.h3m │ │ ├── Plant_Pkinase_fam.hmm.h3p │ │ ├── PlantsPHMM3_89.hmm │ │ ├── PlantsPHMM3_89.hmm.h3f │ │ ├── PlantsPHMM3_89.hmm.h3i │ │ ├── PlantsPHMM3_89.hmm.h3m │ │ ├── PlantsPHMM3_89.hmm.h3p │ │ ├── TF_Rule.txt │ │ ├── TF_selfbuild.hmm │ │ ├── TF_selfbuild.sto │ │ ├── Tfam_domain.hmm │ │ ├── Tfam_domain.hmm.h3f │ │ ├── Tfam_domain.hmm.h3i │ │ ├── Tfam_domain.hmm.h3m │ │ └── Tfam_domain.hmm.h3p │ ├── iTAK.pl │ ├── test_seq │ └── test_seq_output │ │ ├── pk_sequence.fasta │ │ ├── shiu_alignment.txt │ │ ├── shiu_classification.txt │ │ ├── tf_alignment.txt │ │ ├── tf_classification.txt │ │ └── tf_sequence.fasta └── miniprot │ ├── .github │ └── workflows │ │ └── ci.yaml │ ├── .gitignore │ ├── LICENSE.txt │ ├── Makefile │ ├── NEWS.md │ ├── README.md │ ├── align.c │ ├── bseq.c │ ├── chain.c │ ├── format.c │ ├── hit.c │ ├── index.c │ ├── kalloc.c │ ├── kalloc.h │ ├── ketopt.h │ ├── kseq.h │ ├── ksort.h │ ├── kthread.c │ ├── kthread.h │ ├── kvec-km.h │ ├── main.c │ ├── map.c │ ├── miniprot │ ├── miniprot.1 │ ├── miniprot.h │ ├── misc.c │ ├── mppriv.h │ ├── nasw-sse.c │ ├── nasw-tab.c │ ├── nasw.h │ ├── ntseq.c │ ├── options.c │ ├── s2n-lite.h │ ├── sketch.c │ ├── sys.c │ ├── test │ ├── DPP3-hs.gen.fa.gz │ └── DPP3-mm.pep.fa.gz │ └── tex │ ├── Makefile │ ├── bioinfo.cls │ ├── miniprot.bib │ ├── miniprot.tex │ ├── natbib.bst │ └── natbib.sty ├── custom.py ├── doc ├── FAQ.md ├── Installation.md ├── Quick Start.md ├── README.md ├── Usage.md └── What is SynGAP.md ├── dual.py ├── evi.py ├── eviplot.py ├── genepair.py ├── initdb.py ├── master.py ├── scripts ├── Rlabel.py ├── SynGAP_genblastg.py ├── SynGAP_miniprot.py ├── SynGAPcustom_genblastg.py ├── SynGAPcustom_miniprot.py ├── __init__.py ├── __pycache__ │ ├── Rlabel.cpython-310.pyc │ ├── SynGAP_genblastg.cpython-310.pyc │ ├── SynGAP_genblastg.cpython-38.pyc │ ├── SynGAP_miniprot.cpython-310.pyc │ ├── SynGAPcustom_genblastg.cpython-310.pyc │ ├── SynGAPcustom_miniprot.cpython-310.pyc │ ├── __init__.cpython-310.pyc │ ├── __init__.cpython-38.pyc │ ├── anchors_rename.cpython-310.pyc │ ├── findID.cpython-310.pyc │ ├── findnonfunc.cpython-310.pyc │ ├── gapanno_genblastg.cpython-310.pyc │ ├── gapanno_miniprot.cpython-310.pyc │ ├── gapbed.cpython-310.pyc │ ├── gapbed.cpython-38.pyc │ ├── gapfind.cpython-310.pyc │ ├── gapseq.cpython-310.pyc │ ├── gapseq.cpython-38.pyc │ ├── getgenepairs.cpython-310.pyc │ ├── getgenepairs.cpython-38.pyc │ ├── gffgrep.cpython-310.pyc │ ├── gffgrep.cpython-38.pyc │ ├── gffnameback.cpython-310.pyc │ ├── gffnameback.cpython-38.pyc │ ├── gffrename.cpython-310.pyc │ ├── modalign2origin.cpython-310.pyc │ ├── nameback.cpython-310.pyc │ ├── overlapfilter.cpython-310.pyc │ ├── polishtypescan.cpython-310.pyc │ ├── redundantfilter.cpython-310.pyc │ ├── splitmodgff_genblastg.cpython-310.pyc │ └── splitmodgff_miniprot.cpython-310.pyc ├── anchors_rename.py ├── blockR.py ├── findID.py ├── findnonfunc.py ├── gapanno_genblastg.py ├── gapanno_miniprot.py ├── gapbed.py ├── gapfind.py ├── gapseq.py ├── getgenepairs.py ├── gffgrep.py ├── gffnameback.py ├── gffrename.py ├── modalign2origin.py ├── nameback.py ├── overlapfilter.py ├── polishtypescan.py ├── redundantfilter.py ├── splitmodgff_genblastg.py ├── splitmodgff_miniprot.py └── synteny.py ├── syngap └── 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