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Commit 2de80c26 authored by Amandine  PERRIN's avatar Amandine PERRIN
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add licence header for tree module

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#!/usr/bin/env python3 #!/usr/bin/env python3
# coding: utf-8 # coding: utf-8
# ###############################################################################
# This file is part of PanACOTA. #
# #
# Authors: Amandine Perrin #
# Copyright © 2018-2020 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/>. #
# ###############################################################################
""" """
Functions to infer a phylogenetic tree with fastME Functions to infer a phylogenetic tree with fastME
......
#!/usr/bin/env python3 #!/usr/bin/env python3
# coding: utf-8 # coding: utf-8
# ###############################################################################
# This file is part of PanACOTA. #
# #
# Authors: Amandine Perrin #
# Copyright © 2018-2020 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/>. #
# ###############################################################################
""" """
Function to infer a phylogenetic tree from a persistent genome, using FastTree Function to infer a phylogenetic tree from a persistent genome, using FastTree
......
#!/usr/bin/env python3 #!/usr/bin/env python3
# coding: utf-8 # coding: utf-8
# ###############################################################################
# This file is part of PanACOTA. #
# #
# Authors: Amandine Perrin #
# Copyright © 2018-2020 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/>. #
# ###############################################################################
""" """
Function to infer a phylogenetic tree from a persistent genome, using IQtree Function to infer a phylogenetic tree from a persistent genome, using IQtree
......
#!/usr/bin/env python3 #!/usr/bin/env python3
# coding: utf-8 # coding: utf-8
# ###############################################################################
# This file is part of PanACOTA. #
# #
# Authors: Amandine Perrin #
# Copyright © 2018-2020 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/>. #
# ###############################################################################
""" """
Functions to infer a phylogenetic tree with quicktree Functions to infer a phylogenetic tree with quicktree
......
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