├── .DS_Store ├── .gitignore ├── .idea ├── .name ├── Pangloss.iml ├── dictionaries │ ├── charley.xml │ ├── cmccarthy.xml │ └── mbzcgm.xml ├── encodings.xml ├── inspectionProfiles │ └── Project_Default.xml ├── libraries │ └── R_User_Library.xml ├── misc.xml ├── modules.xml ├── perl5local.xml ├── vcs.xml └── workspace.xml ├── BarChart.R ├── Karyotype.R ├── LICENSE.txt ├── Pangloss.py ├── Pangloss ├── BLASTAll.py ├── BUSCO.py ├── ExonerateGene.py ├── GO.py ├── Karyotype.py ├── PAML.py ├── PanGuess.py ├── PanOCT.py ├── QualityCheck.py ├── Size.py ├── Tools.py ├── UpSet.py └── __init__.py ├── Pangloss_Manual.pdf ├── README.md ├── RingChart.R ├── Test_Dataset ├── genomes │ ├── Strain_A.fna │ ├── Strain_B.fna │ ├── dubious.faa │ ├── genomes.txt │ └── reference.faa ├── go.obo ├── goslim_generic.obo ├── saccharomycetales_busco.sh └── testconfig.ini ├── UpSet.R ├── config.ini ├── get_sequence_from_GTF.pl ├── panoct.pl └── test_dataset_config.ini /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/.DS_Store -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/.gitignore -------------------------------------------------------------------------------- /.idea/.name: -------------------------------------------------------------------------------- 1 | Pangloss -------------------------------------------------------------------------------- /.idea/Pangloss.iml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/.idea/Pangloss.iml -------------------------------------------------------------------------------- /.idea/dictionaries/charley.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/.idea/dictionaries/charley.xml -------------------------------------------------------------------------------- /.idea/dictionaries/cmccarthy.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/.idea/dictionaries/cmccarthy.xml -------------------------------------------------------------------------------- /.idea/dictionaries/mbzcgm.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/.idea/dictionaries/mbzcgm.xml -------------------------------------------------------------------------------- /.idea/encodings.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/.idea/encodings.xml -------------------------------------------------------------------------------- /.idea/inspectionProfiles/Project_Default.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/.idea/inspectionProfiles/Project_Default.xml -------------------------------------------------------------------------------- /.idea/libraries/R_User_Library.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/.idea/libraries/R_User_Library.xml -------------------------------------------------------------------------------- /.idea/misc.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/.idea/misc.xml -------------------------------------------------------------------------------- /.idea/modules.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/.idea/modules.xml -------------------------------------------------------------------------------- /.idea/perl5local.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/.idea/perl5local.xml -------------------------------------------------------------------------------- /.idea/vcs.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/.idea/vcs.xml -------------------------------------------------------------------------------- /.idea/workspace.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/.idea/workspace.xml -------------------------------------------------------------------------------- /BarChart.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/BarChart.R -------------------------------------------------------------------------------- /Karyotype.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Karyotype.R -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /Pangloss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Pangloss.py -------------------------------------------------------------------------------- /Pangloss/BLASTAll.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Pangloss/BLASTAll.py -------------------------------------------------------------------------------- /Pangloss/BUSCO.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Pangloss/BUSCO.py -------------------------------------------------------------------------------- /Pangloss/ExonerateGene.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Pangloss/ExonerateGene.py -------------------------------------------------------------------------------- /Pangloss/GO.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Pangloss/GO.py -------------------------------------------------------------------------------- /Pangloss/Karyotype.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Pangloss/Karyotype.py -------------------------------------------------------------------------------- /Pangloss/PAML.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Pangloss/PAML.py -------------------------------------------------------------------------------- /Pangloss/PanGuess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Pangloss/PanGuess.py -------------------------------------------------------------------------------- /Pangloss/PanOCT.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Pangloss/PanOCT.py -------------------------------------------------------------------------------- /Pangloss/QualityCheck.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Pangloss/QualityCheck.py -------------------------------------------------------------------------------- /Pangloss/Size.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Pangloss/Size.py -------------------------------------------------------------------------------- /Pangloss/Tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Pangloss/Tools.py -------------------------------------------------------------------------------- /Pangloss/UpSet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Pangloss/UpSet.py -------------------------------------------------------------------------------- /Pangloss/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Pangloss_Manual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Pangloss_Manual.pdf -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/README.md -------------------------------------------------------------------------------- /RingChart.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/RingChart.R -------------------------------------------------------------------------------- /Test_Dataset/genomes/Strain_A.fna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Test_Dataset/genomes/Strain_A.fna -------------------------------------------------------------------------------- /Test_Dataset/genomes/Strain_B.fna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Test_Dataset/genomes/Strain_B.fna -------------------------------------------------------------------------------- /Test_Dataset/genomes/dubious.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Test_Dataset/genomes/dubious.faa -------------------------------------------------------------------------------- /Test_Dataset/genomes/genomes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Test_Dataset/genomes/genomes.txt -------------------------------------------------------------------------------- /Test_Dataset/genomes/reference.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Test_Dataset/genomes/reference.faa -------------------------------------------------------------------------------- /Test_Dataset/go.obo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Test_Dataset/go.obo -------------------------------------------------------------------------------- /Test_Dataset/goslim_generic.obo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Test_Dataset/goslim_generic.obo -------------------------------------------------------------------------------- /Test_Dataset/saccharomycetales_busco.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Test_Dataset/saccharomycetales_busco.sh -------------------------------------------------------------------------------- /Test_Dataset/testconfig.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/Test_Dataset/testconfig.ini -------------------------------------------------------------------------------- /UpSet.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/UpSet.R -------------------------------------------------------------------------------- /config.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/config.ini -------------------------------------------------------------------------------- /get_sequence_from_GTF.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/get_sequence_from_GTF.pl -------------------------------------------------------------------------------- /panoct.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/panoct.pl -------------------------------------------------------------------------------- /test_dataset_config.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chmccarthy/Pangloss/HEAD/test_dataset_config.ini --------------------------------------------------------------------------------