diff --git a/LICENCE-files/avis-licence.txt b/LICENCE-files/avis-licence.txt new file mode 100644 index 0000000000000000000000000000000000000000..6996ee3cf0aa6819ee259fba2f60da511d2fb10d --- /dev/null +++ b/LICENCE-files/avis-licence.txt @@ -0,0 +1,26 @@ +#!/usr/bin/env python3 +# coding: utf-8 + +############################################################################### + +This file is part of PanACOTA. + +Authors: Amandine Perrin +Copyright © 2016-2018 Institut Pasteur (Paris). +See the COPYRIGHT file for details. + +PanACOTA is a software providing tools for large scale bacterial comparative genomics. From a set of complete and/or draft genomes, you can: + + - Do a quality control of your strains, to eliminate poor quality genomes, which would not give any information for the comparative study + - Uniformly annotate all genomes + - Do a Pan-genome + - Do a Core or Persistent genome + - Align all Core/Persistent families + - Infer a phylogenetic tree from the Core/Persistent families + +PanACOTA is free software: you can redistribute it and/or modify it under the terms of the Affero GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. +PanACOTA is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Affero GNU General Public License for more details. + +You should have received a copy of the Affero GNU General Public License along with PanACOTA (COPYING file). If not, see <https://www.gnu.org/licenses/>. + +############################################################################### \ No newline at end of file diff --git a/LICENCE-files/example-header.png b/LICENCE-files/example-header.png new file mode 100644 index 0000000000000000000000000000000000000000..afd06818b0de38bb79b1d4171a3c402c10467514 Binary files /dev/null and b/LICENCE-files/example-header.png differ diff --git a/LICENCE-files/example-header.txt.md b/LICENCE-files/example-header.txt.md new file mode 100644 index 0000000000000000000000000000000000000000..695ffd561eebc19a64634d72e13c7dd70e72b4b8 --- /dev/null +++ b/LICENCE-files/example-header.txt.md @@ -0,0 +1,18 @@ +$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ +$ $ +$ up so discovery my middleton eagerness dejection explained. Estimating excellence $ +$ ye contrasted insensible as. Oh up unsatiable advantages decisively as a interested. $ +$ Present suppose in esteems in demesne colonel it to. End horrible she landlord $ +$ screened stanhill. Repeated offended you opinions off dissuade ask packages screened. $ +$ She alteration everything sympathize impossible his get compliment. Collected $ +$ few extremity suffering met had sportsman. $ +$ $ +$ Passage its ten led hearted removal cordial. Preference any astonished unreserved $ +$ mrs. Prosperous understood middletons in conviction an uncommonly do. Supposing $ +$ so be resolving breakfast am or perfectly. Is drew am hill from mr. Valley by oh twenty $ +$ direct me so. Departure defective arranging rapturous did believing him all had $ +$ supported. $ +$ Family months lasted simple se nature vulgar him. Picture fo attempt joy excited $ +$ ten carried manners talking how. Suspicion neglected he resolving agreement perceived an. $ +$ $ +$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ \ No newline at end of file diff --git a/LICENCE-files/list-source-files.txt b/LICENCE-files/list-source-files.txt new file mode 100644 index 0000000000000000000000000000000000000000..42bbfb8e4f66d1bb5496cc67b8620dc97f3364cb --- /dev/null +++ b/LICENCE-files/list-source-files.txt @@ -0,0 +1,28 @@ +genomeAPCAT/__init__.py +genomeAPCAT/utils.py +genomeAPCAT/utils_pangenome.py +genomeAPCAT/align_module/__init__.py +genomeAPCAT/align_module/alignment.py +genomeAPCAT/align_module/get_seqs.py +genomeAPCAT/align_module/pan_to_pergenome.py +genomeAPCAT/align_module/post_align.py +genomeAPCAT/annote_module/__init__.py +genomeAPCAT/annote_module/format_functions.py +genomeAPCAT/annote_module/genome_seq_functions.py +genomeAPCAT/annote_module/prokka_functions.py +genomeAPCAT/corepers_module/__init__.py +genomeAPCAT/corepers_module/persistent_functions.py +genomeAPCAT/pangenome_module/__init__.py +genomeAPCAT/pangenome_module/mmseqs_functions.py +genomeAPCAT/pangenome_module/post_treatment.py +genomeAPCAT/pangenome_module/protein_seq_functions.py +genomeAPCAT/subcommands/__init__.py +genomeAPCAT/subcommands/align.py +genomeAPCAT/subcommands/annote.py +genomeAPCAT/subcommands/corepers.py +genomeAPCAT/subcommands/pangenome.py +genomeAPCAT/subcommands/tree.py +genomeAPCAT/tree_module/__init__.py +genomeAPCAT/tree_module/fastme_func.py +genomeAPCAT/tree_module/fasttree_func.py +genomeAPCAT/tree_module/quicktree_func.py