├── .gitignore ├── LICENSE ├── README.md ├── docs ├── .gitignore ├── 404.html ├── Gemfile ├── Gemfile.lock ├── _config.yml ├── _includes │ └── header.html ├── _layouts │ ├── default.html │ ├── home.html │ ├── page.html │ └── post.html ├── _posts │ ├── 2018-01-23-news-and-updates.md │ ├── 2018-02-12-added-some-text.md │ ├── 2018-04-16-more-instructions.md │ ├── 2018-05-09-examples-added.md │ ├── 2018-05-10-prebuilt-databases-added.md │ ├── 2018-05-25-big-push-2.md │ ├── 2018-06-05-add-outgroups.md │ ├── 2018-09-17-pyphlawd-pub.md │ └── 2019-03-11-python3.md ├── about.md ├── assets │ └── img │ │ ├── bait_ex_1.gif │ │ ├── bait_ex_2.gif │ │ ├── bait_ex_3.gif │ │ ├── bait_ex_4.gif │ │ ├── bait_ex_info.png │ │ ├── bait_log.png │ │ ├── clus_ex_1.gif │ │ ├── clus_ex_2.gif │ │ ├── clus_ex_2_fast.gif │ │ ├── clus_ex_3.gif │ │ ├── clus_ex_4.gif │ │ ├── clus_ex_5.gif │ │ ├── clus_ex_info.png │ │ ├── logo.gif │ │ └── pyphlawd_log.png ├── bait_ex.md ├── clustering_ex.md ├── index.md ├── install.md ├── introduction.md ├── other.md ├── runs.md └── scripts.md ├── examples ├── baited │ ├── baits │ │ ├── ITS.fa │ │ ├── matK.fa │ │ ├── rbcL.fa │ │ └── trnLF.fa │ └── notes.md └── clustered │ └── notes.md ├── pyphlawd_log.png ├── pyphlawd_log.psd └── src ├── HTML.py ├── add_clade_clusters.py ├── add_genera_to_paftol_join.py ├── add_internal_seqs_to_clusters.py ├── add_ncbi_to_paftol.py ├── add_outgroup_to_matrix.py ├── add_wcs_columns_taxonomy.py ├── align_tip_clusters.py ├── annotate_clusters.py ├── bad_seqs.py ├── bad_taxa.py ├── bait_clade.py ├── bait_single.py ├── bait_tree.py ├── change_id_to_name_fasta.py ├── change_id_to_name_fasta_mult.py ├── change_id_to_ncbi_fasta.py ├── change_id_to_ncbi_fasta_mult.py ├── change_id_to_ncbi_fasta_mult_wc.py ├── change_name_to_ncbi_tree.py ├── change_ncbi_and_ott_to_names_on_tree.py ├── change_ncbi_to_name_fasta.py ├── change_ncbi_to_name_list.py ├── change_ncbi_to_name_tre.py ├── change_ncbi_to_name_tre_db.py ├── change_ncbi_to_name_tre_fromlist.py ├── change_ncbi_to_name_tre_fromurl.py ├── change_ncbi_to_ott_tre_for_treemerge.py ├── change_ott_to_ncbi_tre_for_figure.py ├── change_tree_names.py ├── change_wcid_to_name_tre_wc.py ├── check_for_programs.py ├── choose_one_species_cluster.py ├── choose_one_species_cluster_fa_aln.py ├── choose_one_species_cluster_fa_aln_and_samp.py ├── choose_one_species_cluster_fa_aln_and_samp_wc.py ├── cluster_all_tips.py ├── cluster_internal.py ├── cluster_internal_wc.py ├── cluster_single.py ├── cluster_single_wc.py ├── cluster_tree.py ├── cluster_tree_wc.py ├── cnode.c ├── cnode.pyx ├── combine_datasets.py ├── combine_paftol_constraints.py ├── combine_trees.py ├── combine_trees_2.py ├── compile_cython.sh ├── conf.py ├── cut_long_internal_branches.py ├── cython_setup.py ├── emoticons.py ├── exclude_desc_patterns.py ├── exclude_patterns.py ├── filter_blast.py ├── find_good_clusters_for_concat.py ├── find_good_clusters_for_concat_batch.py ├── find_good_clusters_for_concat_wc.py ├── generate_table_fasta.py ├── get_all_names.py ├── get_all_ncbi_names.py ├── get_barcodes_for_clade.py ├── get_div_gz.py ├── get_internal_seqs_unrepresented_in_tips.py ├── get_len_seq_summary.py ├── get_min_overlap_multiple_seqs.py ├── get_min_overlap_multiple_seqs_no_tree.py ├── get_ncbi_ids_for_names.py ├── get_ncbi_tax_tree.py ├── get_ncbi_tax_tree_no_species.py ├── get_ncbi_tax_tree_no_species_genus.py ├── get_ncbi_tsv.py ├── get_outlier_bls.py ├── get_outlying_names.py ├── get_subset_genbank.py ├── get_subset_genbank_wc.py ├── join_paftol_tax.py ├── join_paftol_tax2.py ├── join_paftol_tax3.py ├── join_paftol_tax4.py ├── logger.py ├── logo.py ├── make_constraint_from_namealn.py ├── make_constraint_from_ncbialn.py ├── make_constraint_from_ncbialn_wc.py ├── make_dirs.py ├── make_gz_seq_flat.py ├── make_rate_bins.py ├── node.py ├── populate_dirs_first.py ├── populate_dirs_first_wc.py ├── post_process_cluster_info.py ├── process_barcode_blast_results.py ├── process_constraint_aln_toremove.py ├── process_paftol.py ├── pyphlawd_db_maker.py ├── quartet_sampling.py ├── relabel_tree_ncbi_ott.py ├── remake_final_tree.py ├── remove_genomes.py ├── remove_internal_names_in_tree_keep_double.py ├── remove_knuckles.py ├── resolve_tree.py ├── run_all_all_tips.py ├── run_all_polys.py ├── run_overlap_or_qj.py ├── run_post_constraint_test.py ├── seq.py ├── setup_clade_ap.py ├── setup_clade_bait.py ├── setup_clade_wc.py ├── summarize_overlap.py ├── taxalist_from_ncbi.py ├── tree_reader.py ├── tree_utils.py ├── trim_internal_edges.py ├── trim_tips.py ├── trim_tips_and_aln.py ├── update_seqs.py ├── utils.py └── write_fasta_files_from_mcl.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FePhyFoFum/PyPHLAWD/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: 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