LICENSE.txt
MANIFEST.in
README.md
icon.png
requirements.txt
run_tests.py
setup.cfg
setup.py
versioneer.py
ypkpathway.png
docs/make_pdf_manual_using_libreoffice.sh
docs/manual.odt
docs/manual.pdf
docs/pth6.txt
docs/old/1.png
docs/old/2.png
docs/old/3.png
docs/old/4.png
docs/old/5.png
docs/old/6.png
docs/old/Fig 5.png
docs/old/Fig 6.png
docs/old/Screenshot from 2015-07-19.png
docs/old/Supplementary material  II UPDATED.odt
docs/old/Supplementary material  II.docx
docs/old/examples.docx
docs/old/examples.odt
docs/old/examples.txt
docs/old/image.odp
docs/old/pYPK_figure.odt
docs/old/ypkpathway_manual_0_0_8.odt
docs/old/ypkpathway_manual_0_0_9.docx
docs/old/ypkpathway_manual_0_0_9.odt
docs/old/ypkpathway_manual_0_0_9.pdf
docs/pth6/FBA1.gb
docs/pth6/INDATA_pth6.txt
docs/pth6/PDC1.gb
docs/pth6/PGI.gb
docs/pth6/ScTAL1.gb
docs/pth6/ScXKS1.gb
docs/pth6/SsXYL1.gb
docs/pth6/SsXYL2.gb
docs/pth6/TDH3.gb
docs/pth6/TEF1.gb
docs/pth6/log.txt
docs/pth6/new_primers.txt
docs/pth6/pYPK0_FBA1_ScTAL1_PDC1.gb
docs/pth6/pYPK0_FBA1_ScTAL1_PDC1.ipynb
docs/pth6/pYPK0_PGI_ScXKS1_FBA1.gb
docs/pth6/pYPK0_PGI_ScXKS1_FBA1.ipynb
docs/pth6/pYPK0_SsXYL1_SsXYL2_ScXKS1_ScTAL1.gb
docs/pth6/pYPK0_TDH3_SsXYL2_PGI.gb
docs/pth6/pYPK0_TDH3_SsXYL2_PGI.ipynb
docs/pth6/pYPK0_TEF1_SsXYL1_TDH3.gb
docs/pth6/pYPK0_TEF1_SsXYL1_TDH3.ipynb
docs/pth6/pYPK_A.png
docs/pth6/pYPK_ZE.png
docs/pth6/pYPKa.gb
docs/pth6/pYPKa_E_FBA1.gb
docs/pth6/pYPKa_E_PDC1.gb
docs/pth6/pYPKa_E_PGI.gb
docs/pth6/pYPKa_E_TDH3.gb
docs/pth6/pYPKa_E_TEF1.gb
docs/pth6/pYPKa_ZE_FBA1.ipynb
docs/pth6/pYPKa_ZE_PDC1.ipynb
docs/pth6/pYPKa_ZE_PGI.ipynb
docs/pth6/pYPKa_ZE_TDH3.ipynb
docs/pth6/pYPKa_ZE_TEF1.ipynb
docs/pth6/pYPKa_Z_FBA1.gb
docs/pth6/pYPKa_Z_PDC1.gb
docs/pth6/pYPKa_Z_PGI.gb
docs/pth6/pYPKa_Z_TDH3.gb
docs/pth6/pYPKa_Z_TEF1.gb
docs/pth6/pYPKpw.gb
docs/pth6/pw.ipynb
docs/pth6/pw.png
docs/pth6/standard_primers.txt
docs/pth6/start.bat
docs/pth6/start.sh
docs/pth6/tp_g_tp.png
docs/pth6/.ipynb_checkpoints/pw-checkpoint.ipynb
scripts/pth2.txt
scripts/.ipynb_checkpoints/running from command line-checkpoint.ipynb
scripts/.ipynb_checkpoints/running from python-checkpoint.ipynb
scripts/old/generated_notebook.ipynb
scripts/old/ipynb_generator.py
scripts/old/notes on unicode.txt
scripts/old/rerun.ipynb
scripts/old/running from command line.ipynb
scripts/old/running from python.ipynb
scripts/old/ypkpathway.png
scripts/old/ypkpathway_old.py
scripts/old/mypathway/pYPK0_CiGXF1_PsXYL2.gb
scripts/old/mypathway/pYPK0_RPL12Btp_CiGXF1_TDH3tp.gb
scripts/old/mypathway/pYPK0_TDH3tp_PsXYL2_PGI1tp.gb
scripts/old/mypathway/pYPKa.gb
scripts/old/mypathway/pYPKpw.gb
scripts/old/mypathway/primers.fasta
scripts/old/mypathway/pw.ipynb
scripts/old/pth1/pYPK0_CiGXF1_PsXYL2.gb
scripts/old/pth1/pYPK0_RPL12Btp_CiGXF1_TDH3tp.gb
scripts/old/pth1/pYPK0_TDH3tp_PsXYL2_PGI1tp.gb
scripts/old/pth1/pYPKa.gb
scripts/old/pth1/pYPKpw.gb
scripts/old/pth1/primers.fasta
scripts/old/pth1/pw.ipynb
scripts/pth2/INDATA_pth2.txt
scripts/pth2/PGI.gb
scripts/pth2/SsXYL1.gb
scripts/pth2/SsXYL2.gb
scripts/pth2/TDH3.gb
scripts/pth2/TEF1.gb
scripts/pth2/log.txt
scripts/pth2/new_primers.txt
scripts/pth2/pYPK0_SsXYL1_SsXYL2.gb
scripts/pth2/pYPK0_TDH3_SsXYL2_PGI.gb
scripts/pth2/pYPK0_TDH3_SsXYL2_PGI.ipynb
scripts/pth2/pYPK0_TEF1_SsXYL1_TDH3.gb
scripts/pth2/pYPK0_TEF1_SsXYL1_TDH3.ipynb
scripts/pth2/pYPK_A.png
scripts/pth2/pYPK_ZE.png
scripts/pth2/pYPKa.gb
scripts/pth2/pYPKa_E_PGI.gb
scripts/pth2/pYPKa_E_TDH3.gb
scripts/pth2/pYPKa_E_TEF1.gb
scripts/pth2/pYPKa_ZE_PGI.ipynb
scripts/pth2/pYPKa_ZE_TDH3.ipynb
scripts/pth2/pYPKa_ZE_TEF1.ipynb
scripts/pth2/pYPKa_Z_PGI.gb
scripts/pth2/pYPKa_Z_TDH3.gb
scripts/pth2/pYPKa_Z_TEF1.gb
scripts/pth2/pYPKpw.gb
scripts/pth2/pw.ipynb
scripts/pth2/pw.png
scripts/pth2/standard_primers.txt
scripts/pth2/start.bat
scripts/pth2/start.sh
scripts/pth2/tp_g_tp.png
scripts/pth2/.ipynb_checkpoints/pw-checkpoint.ipynb
tests/48_Bek9U1wxXlq1otmE7YHjYpnk.txt
tests/5OxynmwQA3br0cKAG8It7VVNGrg.txt
tests/CB_qLhPgemW0XNLQOQEAdJKFujU.txt
tests/K8z4ijkYa0hA0KEOhv7-6PNJgBM.txt
tests/iM8oDuvJPMPO995IdW3B0oo0Hkc.txt
tests/pth1.txt
tests/pth2.txt
tests/pth3.txt
tests/pth4.txt
tests/pth5.txt
tests/pth6.txt
tests/pth7.txt
tests/test_ypkpathway.py
ypkpathway/__init__.py
ypkpathway/_version.py
ypkpathway/gui.py
ypkpathway/qrc.py
ypkpathway/ypkpathway.py
ypkpathway.egg-info/PKG-INFO
ypkpathway.egg-info/SOURCES.txt
ypkpathway.egg-info/dependency_links.txt
ypkpathway.egg-info/entry_points.txt
ypkpathway.egg-info/not-zip-safe
ypkpathway.egg-info/requires.txt
ypkpathway.egg-info/top_level.txt
ypkpathway/data/nb_template_pYPK0_pw.md
ypkpathway/data/nb_template_pYPK0_tp_gene_tp.md
ypkpathway/data/nb_template_pYPK0_tp_gene_tp_gap_repair.md
ypkpathway/data/nb_template_pYPKa_A_insert.md
ypkpathway/data/nb_template_pYPKa_ZE_insert.md
ypkpathway/data/pYPK0.gb
ypkpathway/data/pYPK_A.png
ypkpathway/data/pYPK_ZE.png
ypkpathway/data/pYPKa.gb
ypkpathway/data/pYPKpw.gb
ypkpathway/data/pw.png
ypkpathway/data/standard_primers.txt
ypkpathway/data/start.bat
ypkpathway/data/start.sh
ypkpathway/data/tp_g_tp.png
ypkpathway/icons/address-book-new.png
ypkpathway/icons/assemble.png
ypkpathway/icons/document-new.png
ypkpathway/icons/document-open.png
ypkpathway/icons/document-save-as.png
ypkpathway/icons/document-save.png
ypkpathway/icons/edit-find-replace.png
ypkpathway/icons/go-home.png
ypkpathway/icons/go-jump.png
ypkpathway/icons/help-browser.png
ypkpathway/icons/ipynb_icon_32x32.png
ypkpathway/icons/media-floppy.png
ypkpathway/icons/preferences-system-session.png
ypkpathway/icons/process-stop.png
ypkpathway/icons/system-log-out.png
ypkpathway/icons/view-refresh.png
ypkpathway/icons/ypkpathway.png