.gitignore
LICENSE.txt
MANIFEST.in
README.md
setup.py
MetaCHIP/BP.py
MetaCHIP/MetaCHIP_add_group_to_tree.R
MetaCHIP/MetaCHIP_circos_HGT.R
MetaCHIP/MetaCHIP_config.py
MetaCHIP/MetaCHIP_phylo.hmm
MetaCHIP/MetaCHIP_phylo_v1.0.0.hmm
MetaCHIP/PI.py
MetaCHIP/Ranger-DTL-Dated.linux
MetaCHIP/Ranger-DTL-Dated.mac
MetaCHIP/SankeyTaxon.py
MetaCHIP/VERSION
MetaCHIP/__init__.py
MetaCHIP/add_group_to_tree.R
MetaCHIP/circos_HGT.py
MetaCHIP/filter_HGT.py
MetaCHIP/get_SCG_tree.py
MetaCHIP/get_flk_gene_functions.py
MetaCHIP/get_sankey_plot.R
MetaCHIP/rename_seqs.py
MetaCHIP/tmp_1.py
MetaCHIP/tmp_2.py
MetaCHIP/tuning_full_length_and_end_match.py
MetaCHIP/update_hmms.py
MetaCHIP.egg-info/PKG-INFO
MetaCHIP.egg-info/SOURCES.txt
MetaCHIP.egg-info/dependency_links.txt
MetaCHIP.egg-info/requires.txt
MetaCHIP.egg-info/top_level.txt
bin/MetaCHIP
images/Combined_trees.png
images/Gene_flow.jpg
images/MetaCHIP_logo.jpg
images/end_match.jpg
images/flanking_regions.png
images/full_length_match.jpg
images/identity_distribution.png
input_file_examples/blastn_js_header.sh
input_file_examples/customized_grouping.txt
input_file_examples/human_gut_bins_GTDB.tsv
input_file_examples/human_gut_bins/bin111.fasta
input_file_examples/human_gut_bins/bin1322.fasta
input_file_examples/human_gut_bins/bin15.fasta
input_file_examples/human_gut_bins/bin27.fasta
input_file_examples/human_gut_bins/bin30.fasta
input_file_examples/human_gut_bins/bin35.fasta
input_file_examples/human_gut_bins/bin51.fasta
input_file_examples/human_gut_bins/bin69.fasta
input_file_examples/human_gut_bins/bin829.fasta
input_file_examples/human_gut_bins/bin96.fasta
manual/Instruction_for_installing_Ranger-DTL2.txt
manual/MetaCHIP_katana users.sh
manual/file_backup/MetaCHIP_User_Manual_v1.0.docx
manual/file_backup/MetaCHIP_User_Manual_v1.0.pdf
manual/file_backup/MetaCHIP_User_Manual_v1.1.10.docx
manual/file_backup/MetaCHIP_User_Manual_v1.1.10.pdf
manual/file_backup/MetaCHIP_User_Manual_v1.1_TT.docx