├── EasySpeciesTree.py ├── README.md ├── example ├── AT.fas ├── Astral.coalescence_tree.nwk ├── Astral.coalescence_tree.pdf ├── Bradi.fas ├── LOC_Os.fas ├── Orthogroups.csv ├── Potri.fas ├── RAxML_bipartitions.concatenation_out.nwk ├── RAxML_bipartitions.concatenation_out.pdf ├── SingleCopyOrthogroups.txt ├── VIT.fas ├── scaffold.fas └── species_id.txt └── run_example.sh /EasySpeciesTree.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dongwei1220/EasySpeciesTree/HEAD/EasySpeciesTree.py -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dongwei1220/EasySpeciesTree/HEAD/README.md -------------------------------------------------------------------------------- /example/AT.fas: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dongwei1220/EasySpeciesTree/HEAD/example/AT.fas -------------------------------------------------------------------------------- /example/Astral.coalescence_tree.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dongwei1220/EasySpeciesTree/HEAD/example/Astral.coalescence_tree.nwk -------------------------------------------------------------------------------- /example/Astral.coalescence_tree.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dongwei1220/EasySpeciesTree/HEAD/example/Astral.coalescence_tree.pdf -------------------------------------------------------------------------------- /example/Bradi.fas: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dongwei1220/EasySpeciesTree/HEAD/example/Bradi.fas -------------------------------------------------------------------------------- /example/LOC_Os.fas: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dongwei1220/EasySpeciesTree/HEAD/example/LOC_Os.fas -------------------------------------------------------------------------------- /example/Orthogroups.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dongwei1220/EasySpeciesTree/HEAD/example/Orthogroups.csv -------------------------------------------------------------------------------- /example/Potri.fas: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dongwei1220/EasySpeciesTree/HEAD/example/Potri.fas -------------------------------------------------------------------------------- /example/RAxML_bipartitions.concatenation_out.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dongwei1220/EasySpeciesTree/HEAD/example/RAxML_bipartitions.concatenation_out.nwk -------------------------------------------------------------------------------- /example/RAxML_bipartitions.concatenation_out.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dongwei1220/EasySpeciesTree/HEAD/example/RAxML_bipartitions.concatenation_out.pdf -------------------------------------------------------------------------------- /example/SingleCopyOrthogroups.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dongwei1220/EasySpeciesTree/HEAD/example/SingleCopyOrthogroups.txt -------------------------------------------------------------------------------- /example/VIT.fas: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dongwei1220/EasySpeciesTree/HEAD/example/VIT.fas -------------------------------------------------------------------------------- /example/scaffold.fas: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dongwei1220/EasySpeciesTree/HEAD/example/scaffold.fas -------------------------------------------------------------------------------- /example/species_id.txt: -------------------------------------------------------------------------------- 1 | AT 2 | Potri 3 | VIT 4 | LOC_Os 5 | Bradi 6 | scaffold 7 | -------------------------------------------------------------------------------- /run_example.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dongwei1220/EasySpeciesTree/HEAD/run_example.sh --------------------------------------------------------------------------------