├── .gitignore ├── AUTHORS ├── COPYING ├── ChangeLog ├── INSTALL ├── Makefile.am ├── Makefile.in ├── NEWS ├── README ├── README.md ├── aclocal.m4 ├── compile ├── compile.mak ├── config.guess ├── config.h.in ├── config.sub ├── configure ├── configure.ac ├── depcomp ├── history.txt ├── images_for_readme ├── BIGE.gif ├── figure1.gif ├── figure2.gif ├── figure3.gif ├── figure4.gif └── table1.gif ├── install-sh ├── missing ├── src ├── Makefile.am ├── Makefile.in ├── ketopt.h ├── tr30dat.c ├── tr30dat.h ├── trf.c ├── trfclean.h └── trfrun.h ├── t ├── diff_cn.fasta ├── diff_cn.fasta.out ├── small_test.fasta ├── small_test.fasta.out ├── test_seqs.fasta └── test_seqs.fasta.out └── test_seqs.txt /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/.gitignore -------------------------------------------------------------------------------- /AUTHORS: -------------------------------------------------------------------------------- 1 | See README.md, section "Authors" 2 | -------------------------------------------------------------------------------- /COPYING: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/COPYING -------------------------------------------------------------------------------- /ChangeLog: -------------------------------------------------------------------------------- 1 | history.txt -------------------------------------------------------------------------------- /INSTALL: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/INSTALL -------------------------------------------------------------------------------- /Makefile.am: -------------------------------------------------------------------------------- 1 | SUBDIRS = src 2 | dist_doc_DATA = README.md 3 | -------------------------------------------------------------------------------- /Makefile.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/Makefile.in -------------------------------------------------------------------------------- /NEWS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/NEWS -------------------------------------------------------------------------------- /README: -------------------------------------------------------------------------------- 1 | README.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/README.md -------------------------------------------------------------------------------- /aclocal.m4: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/aclocal.m4 -------------------------------------------------------------------------------- /compile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/compile -------------------------------------------------------------------------------- /compile.mak: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/compile.mak -------------------------------------------------------------------------------- /config.guess: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/config.guess -------------------------------------------------------------------------------- /config.h.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/config.h.in -------------------------------------------------------------------------------- /config.sub: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/config.sub -------------------------------------------------------------------------------- /configure: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/configure -------------------------------------------------------------------------------- /configure.ac: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/configure.ac -------------------------------------------------------------------------------- /depcomp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/depcomp -------------------------------------------------------------------------------- /history.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/history.txt -------------------------------------------------------------------------------- /images_for_readme/BIGE.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/images_for_readme/BIGE.gif -------------------------------------------------------------------------------- /images_for_readme/figure1.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/images_for_readme/figure1.gif -------------------------------------------------------------------------------- /images_for_readme/figure2.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/images_for_readme/figure2.gif -------------------------------------------------------------------------------- /images_for_readme/figure3.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/images_for_readme/figure3.gif -------------------------------------------------------------------------------- /images_for_readme/figure4.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/images_for_readme/figure4.gif -------------------------------------------------------------------------------- /images_for_readme/table1.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/images_for_readme/table1.gif -------------------------------------------------------------------------------- /install-sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/install-sh -------------------------------------------------------------------------------- /missing: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/missing -------------------------------------------------------------------------------- /src/Makefile.am: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/src/Makefile.am -------------------------------------------------------------------------------- /src/Makefile.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/src/Makefile.in -------------------------------------------------------------------------------- /src/ketopt.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/src/ketopt.h -------------------------------------------------------------------------------- /src/tr30dat.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/src/tr30dat.c -------------------------------------------------------------------------------- /src/tr30dat.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/src/tr30dat.h -------------------------------------------------------------------------------- /src/trf.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/src/trf.c -------------------------------------------------------------------------------- /src/trfclean.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/src/trfclean.h -------------------------------------------------------------------------------- /src/trfrun.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/src/trfrun.h -------------------------------------------------------------------------------- /t/diff_cn.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/t/diff_cn.fasta -------------------------------------------------------------------------------- /t/diff_cn.fasta.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/t/diff_cn.fasta.out -------------------------------------------------------------------------------- /t/small_test.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/t/small_test.fasta -------------------------------------------------------------------------------- /t/small_test.fasta.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/t/small_test.fasta.out -------------------------------------------------------------------------------- /t/test_seqs.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/t/test_seqs.fasta -------------------------------------------------------------------------------- /t/test_seqs.fasta.out: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /test_seqs.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lh3/TRF-mod/HEAD/test_seqs.txt --------------------------------------------------------------------------------