data/gubbins-2.4.1/.gitattributes: ASCII text, with no line terminators data/gubbins-2.4.1/.gitignore: ASCII text data/gubbins-2.4.1/.travis.yml: ASCII text data/gubbins-2.4.1/AUTHORS: ASCII text data/gubbins-2.4.1/CHANGELOG.md: UTF-8 Unicode text data/gubbins-2.4.1/Dockerfile: ASCII text data/gubbins-2.4.1/GubbinsManual_latest.docx: Microsoft Word 2007+ data/gubbins-2.4.1/LICENSE: ASCII text data/gubbins-2.4.1/README.md: UTF-8 Unicode text data/gubbins-2.4.1/VERSION: ASCII text data/gubbins-2.4.1/configure.ac: ASCII text data/gubbins-2.4.1/example_data/PMEN1/PMEN1.branch_base_reconstruction.embl: ASCII text data/gubbins-2.4.1/example_data/PMEN1/PMEN1.filtered_polymorphic_sites.fasta: ASCII text data/gubbins-2.4.1/example_data/PMEN1/PMEN1.filtered_polymorphic_sites.phylip: ASCII text data/gubbins-2.4.1/example_data/PMEN1/PMEN1.final_tree.tre: ASCII text data/gubbins-2.4.1/example_data/PMEN1/PMEN1.node_labelled.tre: ASCII text data/gubbins-2.4.1/example_data/PMEN1/PMEN1.per_branch_statistics.csv: ASCII text data/gubbins-2.4.1/example_data/PMEN1/PMEN1.recombination_predictions.embl: ASCII text data/gubbins-2.4.1/example_data/PMEN1/PMEN1.recombination_predictions.gff: ASCII text data/gubbins-2.4.1/example_data/PMEN1/PMEN1.summary_of_snp_distribution.vcf: Variant Call Format (VCF) version 4.2, ASCII text data/gubbins-2.4.1/example_data/PMEN1/README.md: ASCII text data/gubbins-2.4.1/example_data/ST239/README.md: ASCII text data/gubbins-2.4.1/example_data/ST239/ST239.branch_base_reconstruction.embl: ASCII text data/gubbins-2.4.1/example_data/ST239/ST239.filtered_polymorphic_sites.fasta: ASCII text, with very long lines data/gubbins-2.4.1/example_data/ST239/ST239.filtered_polymorphic_sites.phylip: ASCII text, with very long lines data/gubbins-2.4.1/example_data/ST239/ST239.final_tree.tre: ASCII text, with very long lines data/gubbins-2.4.1/example_data/ST239/ST239.node_labelled.tre: ASCII text, with very long lines data/gubbins-2.4.1/example_data/ST239/ST239.per_branch_statistics.csv: ASCII text data/gubbins-2.4.1/example_data/ST239/ST239.recombination_predictions.embl: ASCII text data/gubbins-2.4.1/example_data/ST239/ST239.recombination_predictions.gff: ASCII text data/gubbins-2.4.1/example_data/ST239/ST239.summary_of_snp_distribution.vcf: Variant Call Format (VCF) version 4.2, ASCII text data/gubbins-2.4.1/install-userspace.sh: Bourne-Again shell script, ASCII text executable data/gubbins-2.4.1/install_dependencies.sh: Bourne-Again shell script, ASCII text executable data/gubbins-2.4.1/m4/ax_pthread.m4: M4 macro processor script, ASCII text data/gubbins-2.4.1/m4/ax_python_devel.m4: M4 macro processor script, ASCII text data/gubbins-2.4.1/obsolete_changelog: ASCII text data/gubbins-2.4.1/python/LICENSE.txt: ASCII text data/gubbins-2.4.1/python/Makefile.am: ASCII text data/gubbins-2.4.1/python/gubbins/PreProcessFasta.py: Python script, ASCII text executable data/gubbins-2.4.1/python/gubbins/ValidateFastaAlignment.py: Python script, ASCII text executable data/gubbins-2.4.1/python/gubbins/__init__.py: Python script, ASCII text executable data/gubbins-2.4.1/python/gubbins/tests/__init__.py: empty data/gubbins-2.4.1/python/gubbins/tests/data/alignment_with_3_sequences.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/alignment_with_too_much_missing_data.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/alignment_with_too_much_missing_data.aln.expected: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/all_unique_sequence_names.fa: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/concatenate_fasta_files.aln.expected: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/destination_tree.tre: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/duplicate_names_in_tree.tre: ASCII text, with very long lines data/gubbins-2.4.1/python/gubbins/tests/data/expected_RAxML_result.multiple_recombinations.iteration_5: ASCII text, with very long lines, with no line terminators data/gubbins-2.4.1/python/gubbins/tests/data/expected_RAxML_result.multiple_recombinations.iteration_5.branch_snps.tab: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/expected_RAxML_result.multiple_recombinations.iteration_5.gff: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/expected_RAxML_result.multiple_recombinations.iteration_5.output_tree: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/expected_RAxML_result.multiple_recombinations.iteration_5.phylip: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/expected_RAxML_result.multiple_recombinations.iteration_5.snp_sites.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/expected_RAxML_result.multiple_recombinations.iteration_5.stats: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/expected_RAxML_result.multiple_recombinations.iteration_5.tab: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/expected_RAxML_result.multiple_recombinations.iteration_5.vcf: Variant Call Format (VCF) version 4.1, ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/expected_final_tree_without_internal_labels.tre: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/expected_multiple_recombinations.aln.start: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/expected_renamed_output_tree: ASCII text, with very long lines data/gubbins-2.4.1/python/gubbins/tests/data/expected_reroot_tree_with_outgroups_all_in_different_clade.tre: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/expected_reroot_tree_with_outgroups_all_in_one_clade.tre: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/expected_reroot_tree_with_outgroups_with_two_mixed_clades.tre: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/expected_rooted_tree.newick: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/expected_test_reroot_tree_with_outgroups_all_in_one_clade_large.tre: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/final_tree_with_internal_labels.tre: ASCII text, with very long lines, with no line terminators data/gubbins-2.4.1/python/gubbins/tests/data/further_alignment.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/gaps_to_be_reinserted.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/gaps_to_be_reinserted.aln.expected: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/gaps_to_be_reinserted.vcf: Variant Call Format (VCF) version 4.1, ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/input_pairwise.aln.phylip: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/input_pairwise.aln.vcf: Variant Call Format (VCF) version 4.1, ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/invalid_newick_tree.tre: ASCII text, with very long lines data/gubbins-2.4.1/python/gubbins/tests/data/iqtree_ancestral.fasta.expected: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/iqtree_ancestral.state: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/multiple_recombinations.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/non_bi_tree.tre: ASCII text, with very long lines data/gubbins-2.4.1/python/gubbins/tests/data/non_bi_tree.tre.expected: ASCII text, with very long lines data/gubbins-2.4.1/python/gubbins/tests/data/non_unique_sequence_names.fa: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/outgroups_input.tre: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/pairwise.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/pairwise.aln.gaps.phylip: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/pairwise.aln.gaps.snp_sites.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/pairwise.aln.gaps.vcf: Variant Call Format (VCF) version 4.1, ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/pairwise.aln.snp_sites.aln_expected: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/pairwise.aln.tre.vcf_expected: Variant Call Format (VCF) version 4.1, ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/pairwise.gaps.snp_sites.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/pairwise.snp_sites.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/pairwise_expected.tre: ASCII text, with no line terminators data/gubbins-2.4.1/python/gubbins/tests/data/pairwise_newick_tree.expected: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/preprocessfasta/all_same_sequence.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/preprocessfasta/expected_missing_data.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/preprocessfasta/expected_multiple_duplicates.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/preprocessfasta/expected_one_duplicate.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/preprocessfasta/missing_data.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/preprocessfasta/multiple_duplicates.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/preprocessfasta/no_duplicates.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/preprocessfasta/one_duplicate.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/raxml_ancestral.fasta.expected: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/raxml_ancestral.state: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/reconvert_fasta_file.aln.expected: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/robinson_foulds_distance_tree1.tre: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/robinson_foulds_distance_tree1.tre.filter_out_removed_taxa_from_tree_expected: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/robinson_foulds_distance_tree1.tre.reroot_at_sequence_4: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/robinson_foulds_distance_tree1.tre.reroot_at_sequence_4_2: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/robinson_foulds_distance_tree1.tre.reroot_tree_at_midpoint_expected: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/robinson_foulds_distance_tree1_dup.tre: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/robinson_foulds_distance_tree2.tre: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/sequence_with_odd_chars.fa: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/sequence_without_a_name.fa: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/sequences_of_different_lengths.fa: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/small_alignment.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/small_recombination.embl: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/small_recombination_different.embl: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/source_tree.tre: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/tree_with_internal_nodes.tre: ASCII text, with no line terminators data/gubbins-2.4.1/python/gubbins/tests/data/tree_with_internal_nodes.tre_expected: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/unrooted_tree.newick: ASCII text, with no line terminators data/gubbins-2.4.1/python/gubbins/tests/data/valid_alignment.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/valid_newick_tree.aln: ASCII text data/gubbins-2.4.1/python/gubbins/tests/data/valid_newick_tree.tre: ASCII text, with very long lines data/gubbins-2.4.1/python/gubbins/tests/test_alignment_python_methods.py: Python script, ASCII text executable data/gubbins-2.4.1/python/gubbins/tests/test_converging_recombinations.py: Python script, ASCII text executable data/gubbins-2.4.1/python/gubbins/tests/test_dependencies.py: Python script, ASCII text executable data/gubbins-2.4.1/python/gubbins/tests/test_pre_process_fasta.py: Python script, ASCII text executable data/gubbins-2.4.1/python/gubbins/tests/test_tree_methods.py: Python script, ASCII text executable data/gubbins-2.4.1/python/gubbins/tests/test_treebuilders.py: Python script, ASCII text executable data/gubbins-2.4.1/python/gubbins/tests/test_utils.py: Python script, ASCII text executable data/gubbins-2.4.1/python/gubbins/tests/test_validate_fasta_input.py: Python script, ASCII text executable data/gubbins-2.4.1/python/gubbins/tests/test_validate_starting_tree.py: Python script, ASCII text executable data/gubbins-2.4.1/python/gubbins/treebuilders.py: Python script, ASCII text executable data/gubbins-2.4.1/python/gubbins/utils.py: Python script, ASCII text executable data/gubbins-2.4.1/python/gubbins/common.py: Python script, ASCII text executable data/gubbins-2.4.1/python/scripts/__init__.py: empty data/gubbins-2.4.1/python/scripts/gubbins_drawer.py: Python script, UTF-8 Unicode text executable data/gubbins-2.4.1/python/scripts/run_gubbins.py: Python script, ASCII text executable data/gubbins-2.4.1/python/setup.py: Python script, ASCII text executable data/gubbins-2.4.1/release/Makefile.am: ASCII text data/gubbins-2.4.1/release/Vagrantfile: ASCII text data/gubbins-2.4.1/release/manifests/trustyvm.pp: ASCII text data/gubbins-2.4.1/src/Makefile.am: ASCII text data/gubbins-2.4.1/src/Newickform.c: C source, ASCII text data/gubbins-2.4.1/src/Newickform.h: C source, ASCII text data/gubbins-2.4.1/src/PyGubbins.cpp: C++ source, ASCII text data/gubbins-2.4.1/src/alignment_file.h: C source, ASCII text data/gubbins-2.4.1/src/block_tab_file.c: C source, ASCII text data/gubbins-2.4.1/src/block_tab_file.h: C source, ASCII text data/gubbins-2.4.1/src/branch_sequences.c: C source, ASCII text, with very long lines data/gubbins-2.4.1/src/branch_sequences.h: C source, ASCII text, with very long lines data/gubbins-2.4.1/src/fasta_of_snp_sites.c: C source, ASCII text data/gubbins-2.4.1/src/fasta_of_snp_sites.h: C source, ASCII text data/gubbins-2.4.1/src/gff_file.c: C source, ASCII text data/gubbins-2.4.1/src/gff_file.h: C source, ASCII text data/gubbins-2.4.1/src/gubbins.c: C source, ASCII text data/gubbins-2.4.1/src/gubbins.h: C source, ASCII text data/gubbins-2.4.1/src/kseq.h: C source, ASCII text data/gubbins-2.4.1/src/parse_phylip.c: C source, ASCII text data/gubbins-2.4.1/src/parse_phylip.h: C source, ASCII text data/gubbins-2.4.1/src/parse_vcf.c: C source, ASCII text data/gubbins-2.4.1/src/parse_vcf.h: C source, ASCII text data/gubbins-2.4.1/src/phylip_of_snp_sites.c: C source, ASCII text data/gubbins-2.4.1/src/phylip_of_snp_sites.h: C source, ASCII text data/gubbins-2.4.1/src/seqUtil.c: C source, ASCII text, with CRLF line terminators data/gubbins-2.4.1/src/seqUtil.h: C source, ASCII text, with CRLF line terminators data/gubbins-2.4.1/src/snp_searching.c: C source, ASCII text data/gubbins-2.4.1/src/snp_searching.h: C source, ASCII text data/gubbins-2.4.1/src/snp_sites.c: C source, ASCII text data/gubbins-2.4.1/src/snp_sites.h: C source, ASCII text data/gubbins-2.4.1/src/string_cat.c: C source, ASCII text data/gubbins-2.4.1/src/string_cat.h: C source, ASCII text data/gubbins-2.4.1/src/tree_scaling.c: C source, ASCII text data/gubbins-2.4.1/src/tree_scaling.h: C source, ASCII text data/gubbins-2.4.1/src/tree_statistics.c: C source, ASCII text data/gubbins-2.4.1/src/tree_statistics.h: C source, ASCII text data/gubbins-2.4.1/src/vcf.c: C source, ASCII text data/gubbins-2.4.1/src/vcf.h: C source, ASCII text data/gubbins-2.4.1/src/alignment_file.c: C source, ASCII text data/gubbins-2.4.1/src/main.c: C source, ASCII text data/gubbins-2.4.1/tests/check_branch_sequences.c: C source, ASCII text data/gubbins-2.4.1/tests/check_branch_sequences.h: C source, ASCII text data/gubbins-2.4.1/tests/check_gubbins.c: C source, ASCII text, with very long lines data/gubbins-2.4.1/tests/check_gubbins.h: C source, ASCII text data/gubbins-2.4.1/tests/check_parse_phylip.c: C source, ASCII text data/gubbins-2.4.1/tests/check_parse_phylip.h: C source, ASCII text data/gubbins-2.4.1/tests/check_snp_searching.c: C source, ASCII text data/gubbins-2.4.1/tests/check_snp_searching.h: C source, ASCII text data/gubbins-2.4.1/tests/check_snp_sites.c: C source, ASCII text, with very long lines data/gubbins-2.4.1/tests/check_snp_sites.h: C source, ASCII text data/gubbins-2.4.1/tests/check_vcf_parsing.c: C source, ASCII text data/gubbins-2.4.1/tests/check_vcf_parsing.h: C source, ASCII text data/gubbins-2.4.1/tests/data/alignment_file_multiple_lines_per_sequence.aln: ASCII text, with very long lines data/gubbins-2.4.1/tests/data/alignment_file_multiple_lines_per_sequence.aln.phylip: ASCII text, with very long lines data/gubbins-2.4.1/tests/data/alignment_file_multiple_lines_per_sequence.aln.snp_sites.aln: ASCII text, with very long lines data/gubbins-2.4.1/tests/data/alignment_file_multiple_lines_per_sequence.aln.vcf: Variant Call Format (VCF) version 4.2, ASCII text, with very long lines data/gubbins-2.4.1/tests/data/alignment_file_one_line_per_sequence.aln: ASCII text, with very long lines data/gubbins-2.4.1/tests/data/alignment_file_one_line_per_sequence.aln.gz: gzip compressed data, was "alignment_file_one_line_per_sequence.aln", last modified: Mon Jan 23 17:10:47 2012, from Unix, original size modulo 2^32 219241 data/gubbins-2.4.1/tests/data/alignment_file_one_line_per_sequence.aln.phylip: ASCII text, with very long lines data/gubbins-2.4.1/tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln: ASCII text, with very long lines data/gubbins-2.4.1/tests/data/alignment_file_one_line_per_sequence.aln.vcf: Variant Call Format (VCF) version 4.2, ASCII text, with very long lines data/gubbins-2.4.1/tests/data/alignment_file_one_line_per_sequence.tre: ASCII text, with very long lines data/gubbins-2.4.1/tests/data/alignment_file_with_large_number_of_snps.aln: ASCII text data/gubbins-2.4.1/tests/data/alignment_file_with_large_number_of_snps.aln.phylip: ASCII text, with very long lines data/gubbins-2.4.1/tests/data/alignment_file_with_large_number_of_snps.aln.snp_sites.aln: ASCII text, with very long lines data/gubbins-2.4.1/tests/data/alignment_file_with_large_number_of_snps.aln.vcf: Variant Call Format (VCF) version 4.2, ASCII text data/gubbins-2.4.1/tests/data/alignment_file_with_n.aln: ASCII text, with very long lines data/gubbins-2.4.1/tests/data/alignment_file_with_n.aln.phylip: ASCII text data/gubbins-2.4.1/tests/data/alignment_file_with_n.aln.snp_sites.aln: ASCII text data/gubbins-2.4.1/tests/data/alignment_file_with_n.aln.vcf: Variant Call Format (VCF) version 4.2, ASCII text, with very long lines data/gubbins-2.4.1/tests/data/alignment_with_gap_in_parent.aln: ASCII text data/gubbins-2.4.1/tests/data/alignment_with_gaps.aln: ASCII text data/gubbins-2.4.1/tests/data/multiple_recombinations.aln: ASCII text data/gubbins-2.4.1/tests/data/multiple_recombinations.aln.phylip: ASCII text data/gubbins-2.4.1/tests/data/multiple_recombinations.aln.snp_sites.aln: ASCII text data/gubbins-2.4.1/tests/data/multiple_recombinations.aln.vcf: Variant Call Format (VCF) version 4.1, ASCII text data/gubbins-2.4.1/tests/data/multiple_recombinations.expected.stats: ASCII text data/gubbins-2.4.1/tests/data/multiple_recombinations.expected.tre: ASCII text, with very long lines, with no line terminators data/gubbins-2.4.1/tests/data/multiple_recombinations.original.tre: ASCII text data/gubbins-2.4.1/tests/data/multiple_recombinations.tre.branch_snps.expected.tab: ASCII text data/gubbins-2.4.1/tests/data/no_recombinations.aln: ASCII text data/gubbins-2.4.1/tests/data/no_recombinations.aln.phylip: ASCII text data/gubbins-2.4.1/tests/data/no_recombinations.aln.snp_sites.aln: ASCII text data/gubbins-2.4.1/tests/data/no_recombinations.aln.vcf: Variant Call Format (VCF) version 4.1, ASCII text data/gubbins-2.4.1/tests/data/no_recombinations.expected.stats: ASCII text data/gubbins-2.4.1/tests/data/no_recombinations.expected.tre: ASCII text, with very long lines, with no line terminators data/gubbins-2.4.1/tests/data/no_recombinations.original.tre: ASCII text, with no line terminators data/gubbins-2.4.1/tests/data/no_recombinations.tre.branch_snps.expected.tab: ASCII text data/gubbins-2.4.1/tests/data/one_recombination.aln: ASCII text data/gubbins-2.4.1/tests/data/one_recombination.aln.phylip: ASCII text data/gubbins-2.4.1/tests/data/one_recombination.aln.snp_sites.aln: ASCII text data/gubbins-2.4.1/tests/data/one_recombination.aln.vcf: Variant Call Format (VCF) version 4.1, ASCII text data/gubbins-2.4.1/tests/data/one_recombination.expected.stats: ASCII text data/gubbins-2.4.1/tests/data/one_recombination.expected.tre: ASCII text, with very long lines, with no line terminators data/gubbins-2.4.1/tests/data/one_recombination.expected.vcf: Variant Call Format (VCF) version 4.1, ASCII text data/gubbins-2.4.1/tests/data/one_recombination.original.tre: ASCII text data/gubbins-2.4.1/tests/data/one_recombination.tre.branch_snps.expected.tab: ASCII text data/gubbins-2.4.1/tests/data/one_recombination.tre.expected.gff: ASCII text data/gubbins-2.4.1/tests/data/one_recombination.tre.expected.tab: ASCII text data/gubbins-2.4.1/tests/data/recombination_at_root/RAxML_result.recombination_at_root.iteration_1: ASCII text, with no line terminators data/gubbins-2.4.1/tests/data/recombination_at_root/RAxML_result.recombination_at_root.iteration_1.original.tre: ASCII text, with no line terminators data/gubbins-2.4.1/tests/data/recombination_at_root/expected_RAxML_result.recombination_at_root.iteration_1.tab: ASCII text data/gubbins-2.4.1/tests/data/recombination_at_root/recombination_at_root.aln: ASCII text data/gubbins-2.4.1/tests/data/recombination_at_root/recombination_at_root.aln.gaps.snp_sites.aln: ASCII text data/gubbins-2.4.1/tests/data/recombination_at_root/recombination_at_root.aln.gaps.vcf: Variant Call Format (VCF) version 4.2, ASCII text data/gubbins-2.4.1/tests/data/small_alignment.aln: ASCII text data/gubbins-2.4.1/tests/data/small_phylip_file.aln: ASCII text data/gubbins-2.4.1/tests/data/two_sequences.aln: ASCII text, with very long lines data/gubbins-2.4.1/tests/data/two_sequences.aln.phylip: ASCII text, with very long lines data/gubbins-2.4.1/tests/data/two_sequences.aln.snp_sites.aln: ASCII text, with very long lines data/gubbins-2.4.1/tests/data/two_sequences.aln.vcf: Variant Call Format (VCF) version 4.2, ASCII text data/gubbins-2.4.1/tests/helper_methods.c: C source, ASCII text data/gubbins-2.4.1/tests/helper_methods.h: C source, ASCII text data/gubbins-2.4.1/tests/makefile: ASCII text, with very long lines data/gubbins-2.4.1/tests/run_all_tests.c: C source, ASCII text data/gubbins-2.4.1/tests/run_tests: Mach-O i386 executable, flags: data/gubbins-2.4.1/debian/changelog: UTF-8 Unicode text data/gubbins-2.4.1/debian/control: UTF-8 Unicode text data/gubbins-2.4.1/debian/copyright: ASCII text data/gubbins-2.4.1/debian/gubbins_drawer.1: troff or preprocessor input, ASCII text data/gubbins-2.4.1/debian/install: ASCII text data/gubbins-2.4.1/debian/links: ASCII text data/gubbins-2.4.1/debian/lintian-overrides: ASCII text data/gubbins-2.4.1/debian/manpages: ASCII text data/gubbins-2.4.1/debian/patches/do_not_handle_python_by_upstream_build_system.patch: unified diff output, ASCII text data/gubbins-2.4.1/debian/patches/gubbins_exe_in_usr_lib.patch: unified diff output, ASCII text data/gubbins-2.4.1/debian/patches/series: ASCII text data/gubbins-2.4.1/debian/patches/spelling-error-in-binary.patch: unified diff output, UTF-8 Unicode text data/gubbins-2.4.1/debian/rules: a /usr/bin/make -f script, ASCII text executable data/gubbins-2.4.1/debian/run_gubbins.1: troff or preprocessor input, ASCII text data/gubbins-2.4.1/debian/salsa-ci.yml: ASCII text data/gubbins-2.4.1/debian/source/format: ASCII text data/gubbins-2.4.1/debian/tests/control: ASCII text data/gubbins-2.4.1/debian/tests/run-example: POSIX shell script, ASCII text executable data/gubbins-2.4.1/debian/upstream/metadata: ASCII text data/gubbins-2.4.1/debian/watch: ASCII text data/gubbins-2.4.1/.pc/.version: ASCII text data/gubbins-2.4.1/.pc/.quilt_patches: ASCII text data/gubbins-2.4.1/.pc/.quilt_series: ASCII text data/gubbins-2.4.1/.pc/applied-patches: ASCII text data/gubbins-2.4.1/.pc/do_not_handle_python_by_upstream_build_system.patch/Makefile.am: automake makefile script, ASCII text data/gubbins-2.4.1/.pc/gubbins_exe_in_usr_lib.patch/src/main.c: C source, ASCII text data/gubbins-2.4.1/.pc/gubbins_exe_in_usr_lib.patch/python/gubbins/common.py: Python script, ASCII text executable data/gubbins-2.4.1/.pc/spelling-error-in-binary.patch/src/alignment_file.c: C source, ASCII text data/gubbins-2.4.1/.pc/spelling-error-in-binary.patch/src/main.c: C source, ASCII text data/gubbins-2.4.1/Makefile.am: automake makefile script, ASCII text