data/baitfisher-1.2.7+git20190123.241d060+dfsg/CAligner/CAligner.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/CBaitRecord.h: C++ source, ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/CBlastParser.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/CDistance_matrix.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/CDnaString2.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/CFile/CFile2_1.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/CHistogram.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/CRequiredTaxon.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/CSeqNameList.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/CSequence_Mol2_1.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/CSequences2.h: C++ source, ASCII text, with CRLF, LF line terminators data/baitfisher-1.2.7+git20190123.241d060+dfsg/CSplit2.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/CTaxonNamesDictionary.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Csequence_cluster_and_center_sequence.cpp: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Csequence_cluster_and_center_sequence.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Ctriple.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/DEBUG_STUFF.h: C source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Documentation/BaitFisher-BaitFilter-Manual.pdf: PDF document, version 1.4 data/baitfisher-1.2.7+git20190123.241d060+dfsg/Documentation/BaitFisher-BaitFilter-Manual.tex: LaTeX 2e document, UTF-8 Unicode text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV10520-RA_2_8_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV10520-RA_3_8_all.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV10520-RA_4_8_all.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV10520-RA_5_8_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV10520-RA_6_8_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV10520-RA_7_8_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV10520-RA_8_8_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV11525-RA_1_2_all.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV13343-RA_2_5_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV13343-RA_3_5_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV13343-RA_4_5_all.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV13343-RA_5_5_all.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV13708-RA_2_3_all.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV13708-RA_3_3_all.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV13720-RA_11_12_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV13720-RA_2_12_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV13720-RA_4_12_all.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV13720-RA_6_12_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV13720-RA_7_12_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV16710-RA_2_7_all.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV16710-RA_3_7_all.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV16710-RA_5_7_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV16710-RA_6_7_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV16747-RA_11_15_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV16747-RA_12_15_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV16747-RA_2_15_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV16747-RA_3_15_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV16747-RA_4_15_all.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV16747-RA_6_15_all.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV16747-RA_8_15_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV18410-RA_2_6_all.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV18410-RA_3_6_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV18410-RA_4_6_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/NV18410-RA_5_6_all.fas: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/BaitFisher-results/loci_baits.txt: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/Nvit-genome/Nvit_1.0_scaffolds_reduced.fa: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/Nvit-genome/Nvit_OGSv1.2_reduced.gff2: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/README: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/alignments/EOG5B2RVS.linsi.nt_without_bees_ants_rmgo.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/alignments/EOG5B2RVT.linsi.nt_without_bees_ants_rmgo.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/alignments/EOG5ZPCSX.linsi.nt_without_bees_ants_rmgo.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/alignments/EOG5ZPCT0.linsi.nt_without_bees_ants_rmgo.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/alignments/EOG5ZW48P.linsi.nt_without_bees_ants_rmgo.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/parameterfile.txt: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/runner.log: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-with-alignment-cutting-and-required-taxa/run-example.sh: POSIX shell script, ASCII text executable data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-without-alignment-cutting/BaitFilter-analysis/run-BaitFilter.sh: POSIX shell script, ASCII text executable data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-without-alignment-cutting/alignments/EOG505R03.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-without-alignment-cutting/alignments/EOG57H4P2.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-without-alignment-cutting/alignments/EOG5DV4JW.fas: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-without-alignment-cutting/parameter.txt: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/Example/Example-without-alignment-cutting/run-example.sh: POSIX shell script, ASCII text executable data/baitfisher-1.2.7+git20190123.241d060+dfsg/GFF-class.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/GFF-collection.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/LICENSE.GPLv3.txt: UTF-8 Unicode (with BOM) text data/baitfisher-1.2.7+git20190123.241d060+dfsg/LICENSE.md: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/LICENSE_AND_COPYRIGHT_as_found_in_each_source_file: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/README.md: UTF-8 Unicode (with BOM) text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/VERSION_HISTORY.md: ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/bait-filter.cpp: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/bait-fisher-helper.cpp: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/bait-fisher-helper.h: C source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/bait-fisher.cpp: C++ source, ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/basic-DNA-RNA-AA-routines.h: C source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/easystring.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/fast-dynamic-bitset/fast-dynamic-bitset.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/fast-realloc-vector.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/faststring2.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/global-types-and-parameters.cpp: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/global-types-and-parameters.h: C source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/makefile: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/makefile_win: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/mydir-unix.cpp: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/mydir-unix.h: C source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/primefactors.h: C source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/print_container.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/range_functions.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/scoring-matrices/CScoreMatrix.h: C++ source, ASCII text, with very long lines data/baitfisher-1.2.7+git20190123.241d060+dfsg/simpledna_N0.mat: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/statistic_functions.h: C++ source, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/typedefs.h: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/baitfisher.docs: empty data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/baitfisher.examples: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/baitfisher.manpages: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/changelog: UTF-8 Unicode text data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/control: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/copyright: UTF-8 Unicode text data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/dirs: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/docs: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/lintian-overrides: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/patches/fix_example.patch: unified diff output, ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/patches/series: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/rules: a /usr/bin/make -f script, ASCII text executable data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/salsa-ci.yml: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/source/format: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/tests/control: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/tests/run-unit-test: Bourne-Again shell script, ASCII text executable data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/upstream/metadata: UTF-8 Unicode text data/baitfisher-1.2.7+git20190123.241d060+dfsg/debian/watch: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/.pc/.version: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/.pc/.quilt_patches: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/.pc/.quilt_series: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/.pc/applied-patches: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/.pc/fix_example.patch/Example/Example-without-alignment-cutting/run-example.sh: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/.pc/fix_example.patch/Example/Example-without-alignment-cutting/BaitFilter-analysis/run-BaitFilter.sh: ASCII text data/baitfisher-1.2.7+git20190123.241d060+dfsg/.pc/fix_example.patch/Example/Example-with-alignment-cutting-and-required-taxa/run-example.sh: ASCII text