├── .github └── workflows │ └── main.yml ├── .gitignore ├── LICENSE ├── README.md ├── emmaemb ├── __init__.py ├── config.py ├── core.py ├── find_all_pla2g2_embeddings.py ├── functions.py ├── test.py └── vizualisation.py ├── examples ├── Pla2g2 │ ├── Pla2g2.fasta │ ├── Pla2g2_emma.py │ ├── Pla2g2_features.csv │ ├── README.md │ ├── embeddings │ │ ├── ESMC │ │ │ ├── bAncyB.npy │ │ │ ├── bAncyC.npy │ │ │ ├── bAncyD.npy │ │ │ ├── bAncyE.npy │ │ │ ├── bAnplB.npy │ │ │ ├── bAnplC.npy │ │ │ ├── bAnplD.npy │ │ │ ├── bAnplE.npy │ │ │ ├── bApauC.npy │ │ │ ├── bApfoB.npy │ │ │ ├── bApfoC.npy │ │ │ ├── bApfoD.npy │ │ │ ├── bApfoE.npy │ │ │ ├── bAqchB.npy │ │ │ ├── bAqchC.npy │ │ │ ├── bAqchD.npy │ │ │ ├── bBareB.npy │ │ │ ├── bBareC.npy │ │ │ ├── bBareD.npy │ │ │ ├── bBareE.npy │ │ │ ├── bChmaB.npy │ │ │ ├── bChmaC.npy │ │ │ ├── bChmaD.npy │ │ │ ├── bChmaE.npy │ │ │ ├── bCocoD.npy │ │ │ ├── bCocoE.npy │ │ │ ├── bCucaB.npy │ │ │ ├── bCucaC.npy │ │ │ ├── bCucaD3.npy │ │ │ ├── bGagaB.npy │ │ │ ├── bGagaC.npy │ │ │ ├── bGagaD.npy │ │ │ ├── bGagaE.npy │ │ │ ├── bHaleB.npy │ │ │ ├── bHaleC.npy │ │ │ ├── bHaleD.npy │ │ │ ├── bNaauB.npy │ │ │ ├── bNaauC.npy │ │ │ ├── bNaauD.npy │ │ │ ├── bOphoC.npy │ │ │ ├── bOphoD.npy │ │ │ ├── bOphoE.npy │ │ │ ├── bPafaB.npy │ │ │ ├── bPafaC.npy │ │ │ ├── bPafaD.npy │ │ │ ├── bPskrB.npy │ │ │ ├── bPskrC.npy │ │ │ ├── bPskrD.npy │ │ │ ├── bPskrE.npy │ │ │ ├── bPyadB.npy │ │ │ ├── bPyadC.npy │ │ │ ├── bPyadD.npy │ │ │ ├── bSecoD.npy │ │ │ ├── bSecoE.npy │ │ │ ├── bStocB.npy │ │ │ ├── bStocC.npy │ │ │ ├── bStocD.npy │ │ │ ├── bStocE.npy │ │ │ ├── bUrpeB.npy │ │ │ ├── bUrpeC.npy │ │ │ ├── bUrpeD.npy │ │ │ ├── cAlmiC.npy │ │ │ ├── cAlmiD1.npy │ │ │ ├── cAlmiD3.npy │ │ │ ├── cAlmiE.npy │ │ │ ├── cAlsiC.npy │ │ │ ├── cAlsiD3.npy │ │ │ ├── cChmyD1.npy │ │ │ ├── cChmyD3.npy │ │ │ ├── cChmyF.npy │ │ │ ├── cChpiD1.npy │ │ │ ├── cChpiD2.npy │ │ │ ├── cChpiD3.npy │ │ │ ├── cChpiF.npy │ │ │ ├── cCrpoC.npy │ │ │ ├── cCrpoD1.npy │ │ │ ├── cCrpoD3.npy │ │ │ ├── cCrpoE.npy │ │ │ ├── cGavganC.npy │ │ │ ├── cGavganD1.npy │ │ │ ├── cGavganD3.npy │ │ │ ├── cGavganE.npy │ │ │ ├── cGoagD1.npy │ │ │ ├── cGoagD2.npy │ │ │ ├── cGoagD3.npy │ │ │ ├── cGoagE.npy │ │ │ ├── cGoagF.npy │ │ │ ├── cPesiD1.npy │ │ │ ├── cPesiD2.npy │ │ │ ├── cPesiD3.npy │ │ │ ├── cPesiE.npy │ │ │ ├── cPesiF.npy │ │ │ ├── mAifuC.npy │ │ │ ├── mAifuD.npy │ │ │ ├── mAifuE.npy │ │ │ ├── mAifuF.npy │ │ │ ├── mAifuV.npy │ │ │ ├── mAimeC.npy │ │ │ ├── mAimeDa.npy │ │ │ ├── mAimeDb.npy │ │ │ ├── mAimeE.npy │ │ │ ├── mAimeF.npy │ │ │ ├── mBibiA2.npy │ │ │ ├── mBibiA3.npy │ │ │ ├── mBibiA4.npy │ │ │ ├── mBibiC.npy │ │ │ ├── mBibiDa.npy │ │ │ ├── mBibiDb.npy │ │ │ ├── mBibiE.npy │ │ │ ├── mBibiF.npy │ │ │ ├── mBotaA.npy │ │ │ ├── mBotaA3.npy │ │ │ ├── mBotaA5.npy │ │ │ ├── mBotaC.npy │ │ │ ├── mBotaDa.npy │ │ │ ├── mBotaDb.npy │ │ │ ├── mBotaF.npy │ │ │ ├── mBotaV.npy │ │ │ ├── mCahiA.npy │ │ │ ├── mCahiA2.npy │ │ │ ├── mCahiA4.npy │ │ │ ├── mCahiA5.npy │ │ │ ├── mCahiC.npy │ │ │ ├── mCahiDa.npy │ │ │ ├── mCahiDb.npy │ │ │ ├── mCahiE.npy │ │ │ ├── mCahiF.npy │ │ │ ├── mCahiV.npy │ │ │ ├── mCaluC.npy │ │ │ ├── mCaluD1.npy │ │ │ ├── mCaluE.npy │ │ │ ├── mCaluF.npy │ │ │ ├── mCaluV.npy │ │ │ ├── mChlaA2.npy │ │ │ ├── mChlaA3.npy │ │ │ ├── mChlaA4.npy │ │ │ ├── mChlaC.npy │ │ │ ├── mChlaD.npy │ │ │ ├── mChlaE.npy │ │ │ ├── mChlaF.npy │ │ │ ├── mChlaV.npy │ │ │ ├── mCocrA2.npy │ │ │ ├── mCocrA3.npy │ │ │ ├── mCocrD.npy │ │ │ ├── mCocrE.npy │ │ │ ├── mCocrF.npy │ │ │ ├── mCocrV.npy │ │ │ ├── mDanoA.npy │ │ │ ├── mDanoC.npy │ │ │ ├── mDanoD.npy │ │ │ ├── mDanoF.npy │ │ │ ├── mDanoV.npy │ │ │ ├── mEledA1.npy │ │ │ ├── mEledA2.npy │ │ │ ├── mEledA3.npy │ │ │ ├── mEledD1.npy │ │ │ ├── mEledE.npy │ │ │ ├── mEledF.npy │ │ │ ├── mEledV.npy │ │ │ ├── mEnluC.npy │ │ │ ├── mEnluD1.npy │ │ │ ├── mEnluE.npy │ │ │ ├── mEnluF.npy │ │ │ ├── mEnluV.npy │ │ │ ├── mEqcaA.npy │ │ │ ├── mEqcaC.npy │ │ │ ├── mEqcaD.npy │ │ │ ├── mEqcaE.npy │ │ │ ├── mEqcaF.npy │ │ │ ├── mEqcaV.npy │ │ │ ├── mEreuA1.npy │ │ │ ├── mEreuA10.npy │ │ │ ├── mEreuA11.npy │ │ │ ├── mEreuA12.npy │ │ │ ├── mEreuA13.npy │ │ │ ├── mEreuA14.npy │ │ │ ├── mEreuA15.npy │ │ │ ├── mEreuA2.npy │ │ │ ├── mEreuA3.npy │ │ │ ├── mEreuA5.npy │ │ │ ├── mEreuA6.npy │ │ │ ├── mEreuA7.npy │ │ │ ├── mEreuA8.npy │ │ │ ├── mEreuA9.npy │ │ │ ├── mEreuC.npy │ │ │ ├── mEreuD1.npy │ │ │ ├── mEreuE.npy │ │ │ ├── mEreuF.npy │ │ │ ├── mEreuV.npy │ │ │ ├── mFecaD.npy │ │ │ ├── mFecaE.npy │ │ │ ├── mFecaF.npy │ │ │ ├── mFecaV.npy │ │ │ ├── mHeglA1.npy │ │ │ ├── mHeglA2.npy │ │ │ ├── mHeglA3.npy │ │ │ ├── mHeglD.npy │ │ │ ├── mHeglE.npy │ │ │ ├── mHeglF.npy │ │ │ ├── mHeglV.npy │ │ │ ├── mHosaA.npy │ │ │ ├── mHosaD.npy │ │ │ ├── mHosaE.npy │ │ │ ├── mHosaF.npy │ │ │ ├── mHosaV.npy │ │ │ ├── mLoafA1.npy │ │ │ ├── mLoafA2.npy │ │ │ ├── mLoafC.npy │ │ │ ├── mLoafD.npy │ │ │ ├── mLoafE.npy │ │ │ ├── mLoafF.npy │ │ │ ├── mLoafV.npy │ │ │ ├── mMamaA1.npy │ │ │ ├── mMamaD.npy │ │ │ ├── mMamaE.npy │ │ │ ├── mMamaF.npy │ │ │ ├── mMamaV.npy │ │ │ ├── mMimuA.npy │ │ │ ├── mMimuC.npy │ │ │ ├── mMimuD.npy │ │ │ ├── mMimuE.npy │ │ │ ├── mMimuF.npy │ │ │ ├── mMimuV.npy │ │ │ ├── mModoC.npy │ │ │ ├── mModoD.npy │ │ │ ├── mModoE.npy │ │ │ ├── mModoF.npy │ │ │ ├── mModoV1.npy │ │ │ ├── mModoV2.npy │ │ │ ├── mMumuA.npy │ │ │ ├── mMumuC.npy │ │ │ ├── mMumuD1.npy │ │ │ ├── mMumuE.npy │ │ │ ├── mMumuF.npy │ │ │ ├── mMumuV1.npy │ │ │ ├── mMupuC.npy │ │ │ ├── mMupuD.npy │ │ │ ├── mMupuE.npy │ │ │ ├── mMupuF.npy │ │ │ ├── mMupuV.npy │ │ │ ├── mMyluA1.npy │ │ │ ├── mMyluA2.npy │ │ │ ├── mMyluA4.npy │ │ │ ├── mMyluC.npy │ │ │ ├── mMyluD.npy │ │ │ ├── mMyluE.npy │ │ │ ├── mMyluF.npy │ │ │ ├── mMyluV.npy │ │ │ ├── mNescD.npy │ │ │ ├── mNescE.npy │ │ │ ├── mNescF.npy │ │ │ ├── mNescV.npy │ │ │ ├── mOcprA1.npy │ │ │ ├── mOcprA2.npy │ │ │ ├── mOcprA3.npy │ │ │ ├── mOcprC.npy │ │ │ ├── mOcprD.npy │ │ │ ├── mOcprE.npy │ │ │ ├── mOcprF.npy │ │ │ ├── mOcprV.npy │ │ │ ├── mOdviA1.npy │ │ │ ├── mOdviA2.npy │ │ │ ├── mOdviA3.npy │ │ │ ├── mOdviC.npy │ │ │ ├── mOdviD.npy │ │ │ ├── mOdviE.npy │ │ │ ├── mOdviF.npy │ │ │ ├── mOdviV.npy │ │ │ ├── mOran2.npy │ │ │ ├── mOran4.npy │ │ │ ├── mOranD.npy │ │ │ ├── mOranE.npy │ │ │ ├── mOranF.npy │ │ │ ├── mOrcuA.npy │ │ │ ├── mOrcuA2.npy │ │ │ ├── mOrcuA3.npy │ │ │ ├── mOrcuA4.npy │ │ │ ├── mOrcuC.npy │ │ │ ├── mOrcuD.npy │ │ │ ├── mOrcuE.npy │ │ │ ├── mOrcuF.npy │ │ │ ├── mOrcuV.npy │ │ │ ├── mOrorC.npy │ │ │ ├── mOrorD.npy │ │ │ ├── mOrorE.npy │ │ │ ├── mOrorV.npy │ │ │ ├── mOvarA1.npy │ │ │ ├── mOvarA2.npy │ │ │ ├── mOvarA3.npy │ │ │ ├── mOvarC.npy │ │ │ ├── mOvarD.npy │ │ │ ├── mOvarF.npy │ │ │ ├── mPahoA1.npy │ │ │ ├── mPahoA3.npy │ │ │ ├── mPahoA5.npy │ │ │ ├── mPahoC.npy │ │ │ ├── mPahoD.npy │ │ │ ├── mPahoE.npy │ │ │ ├── mPahoF.npy │ │ │ ├── mPahoV.npy │ │ │ ├── mPatiC.npy │ │ │ ├── mPatiD.npy │ │ │ ├── mPatiE.npy │ │ │ ├── mPatiF.npy │ │ │ ├── mPatiV.npy │ │ │ ├── mPhciC.npy │ │ │ ├── mPhciDa.npy │ │ │ ├── mPhciDb.npy │ │ │ ├── mPhciE.npy │ │ │ ├── mPhciF.npy │ │ │ ├── mPhciV1.npy │ │ │ ├── mPhciV2.npy │ │ │ ├── mPhciV3.npy │ │ │ ├── mPtvaC.npy │ │ │ ├── mPtvaD.npy │ │ │ ├── mPtvaE.npy │ │ │ ├── mPtvaF.npy │ │ │ ├── mPtvaV.npy │ │ │ ├── mSahaC.npy │ │ │ ├── mSahaD.npy │ │ │ ├── mSahaE.npy │ │ │ ├── mSahaF.npy │ │ │ ├── mSahaV1.npy │ │ │ ├── mSahaV2.npy │ │ │ ├── mSahaV4.npy │ │ │ ├── mSahaV5.npy │ │ │ ├── mSoarA2.npy │ │ │ ├── mSoarA3.npy │ │ │ ├── mSoarC.npy │ │ │ ├── mSoarD.npy │ │ │ ├── mSoarE.npy │ │ │ ├── mSoarF.npy │ │ │ ├── mSoarV.npy │ │ │ ├── mTrmaA2.npy │ │ │ ├── mTrmaC.npy │ │ │ ├── mTrmaD.npy │ │ │ ├── mTrmaE.npy │ │ │ ├── mTrmaF.npy │ │ │ ├── mTrmaV.npy │ │ │ ├── mUrmaC.npy │ │ │ ├── mUrmaD.npy │ │ │ ├── mUrmaV.npy │ │ │ ├── sBocoD.npy │ │ │ ├── sBocoE.npy │ │ │ ├── sBocoF.npy │ │ │ ├── sBocoGo.npy │ │ │ ├── sCradD.npy │ │ │ ├── sCradE.npy │ │ │ ├── sCradF.npy │ │ │ ├── sCradGa.npy │ │ │ ├── sCradGc.npy │ │ │ ├── sCratE.npy │ │ │ ├── sCratF.npy │ │ │ ├── sCratGa.npy │ │ │ ├── sCratGb.npy │ │ │ ├── sCratGc.npy │ │ │ ├── sCratGk49.npy │ │ │ ├── sCrheAE.npy │ │ │ ├── sCrheAF.npy │ │ │ ├── sCrheAGa1.npy │ │ │ ├── sCrheAGa2.npy │ │ │ ├── sCrheAGb.npy │ │ │ ├── sCrheAGc1.npy │ │ │ ├── sCrheBE.npy │ │ │ ├── sCrheBF.npy │ │ │ ├── sCrheBGa1.npy │ │ │ ├── sCrhoAF.npy │ │ │ ├── sCrhoAGa1.npy │ │ │ ├── sCrhoAGa2.npy │ │ │ ├── sCrhoAGb.npy │ │ │ ├── sCrhoAGc1.npy │ │ │ ├── sCrhoBD.npy │ │ │ ├── sCrhoBE.npy │ │ │ ├── sCrhoBF.npy │ │ │ ├── sCrhoBGc1.npy │ │ │ ├── sCrhoGa.npy │ │ │ ├── sCrhoGc.npy │ │ │ ├── sCrscAE.npy │ │ │ ├── sCrscAF.npy │ │ │ ├── sCrscAGa1.npy │ │ │ ├── sCrscAGa2.npy │ │ │ ├── sCrscAGb.npy │ │ │ ├── sCrscAGc1.npy │ │ │ ├── sCrscAGc2.npy │ │ │ ├── sCrscBE.npy │ │ │ ├── sCrscBF.npy │ │ │ ├── sCrscBGa1.npy │ │ │ ├── sCrscBGb.npy │ │ │ ├── sCrscBGc1.npy │ │ │ ├── sCrscBGk49.npy │ │ │ ├── sDeacE.npy │ │ │ ├── sDeacF.npy │ │ │ ├── sDeacGa.npy │ │ │ ├── sDeacGb.npy │ │ │ ├── sDeacGc.npy │ │ │ ├── sDeacGk49.npy │ │ │ ├── sLabiD.npy │ │ │ ├── sLabiE.npy │ │ │ ├── sLabiF.npy │ │ │ ├── sLabiGo.npy │ │ │ ├── sLaviD.npy │ │ │ ├── sLaviE.npy │ │ │ ├── sLaviF.npy │ │ │ ├── sLaviGo.npy │ │ │ ├── sNoscD.npy │ │ │ ├── sNoscE.npy │ │ │ ├── sNoscF.npy │ │ │ ├── sNoscGc.npy │ │ │ ├── sOpgrDb.npy │ │ │ ├── sOpgrF.npy │ │ │ ├── sOpgrG0.npy │ │ │ ├── sOphaD.npy │ │ │ ├── sOphaE.npy │ │ │ ├── sOphaF.npy │ │ │ ├── sOphaGc.npy │ │ │ ├── sPapiE.npy │ │ │ ├── sPapiF.npy │ │ │ ├── sPapiG0.npy │ │ │ ├── sPoviD.npy │ │ │ ├── sPoviE.npy │ │ │ ├── sPoviF.npy │ │ │ ├── sPoviG0.npy │ │ │ ├── sPrflE.npy │ │ │ ├── sPrflGa1.npy │ │ │ ├── sPrflGa2.npy │ │ │ ├── sPrflGb.npy │ │ │ ├── sPrflGck.npy │ │ │ ├── sPrflGk49.npy │ │ │ ├── sPrmuE.npy │ │ │ ├── sPrmuF.npy │ │ │ ├── sPrmuGa1.npy │ │ │ ├── sPrmuGa2.npy │ │ │ ├── sPrmuGb.npy │ │ │ ├── sPrmuGck.npy │ │ │ ├── sPrmuGk49.npy │ │ │ ├── sPsteD.npy │ │ │ ├── sPsteE.npy │ │ │ ├── sPsteF.npy │ │ │ ├── sPsteGc.npy │ │ │ ├── sPybiE.npy │ │ │ ├── sPybiF.npy │ │ │ ├── sVibeEa.npy │ │ │ ├── sVibeF.npy │ │ │ ├── sVibeGa1.npy │ │ │ ├── sVibeGa2.npy │ │ │ └── sVibeGa4.npy │ │ └── ProtT5 │ │ │ ├── bAncyB.npy │ │ │ ├── bAncyC.npy │ │ │ ├── bAncyD.npy │ │ │ ├── bAncyE.npy │ │ │ ├── bAnplB.npy │ │ │ ├── bAnplC.npy │ │ │ ├── bAnplD.npy │ │ │ ├── bAnplE.npy │ │ │ ├── bApauC.npy │ │ │ ├── bApfoB.npy │ │ │ ├── bApfoC.npy │ │ │ ├── bApfoD.npy │ │ │ ├── bApfoE.npy │ │ │ ├── bAqchB.npy │ │ │ ├── bAqchC.npy │ │ │ ├── bAqchD.npy │ │ │ ├── bBareB.npy │ │ │ ├── bBareC.npy │ │ │ ├── bBareD.npy │ │ │ ├── bBareE.npy │ │ │ ├── bChmaB.npy │ │ │ ├── bChmaC.npy │ │ │ ├── bChmaD.npy │ │ │ ├── bChmaE.npy │ │ │ ├── bCocoD.npy │ │ │ ├── bCocoE.npy │ │ │ ├── bCucaB.npy │ │ │ ├── bCucaC.npy │ │ │ ├── bCucaD3.npy │ │ │ ├── bGagaB.npy │ │ │ ├── bGagaC.npy │ │ │ ├── bGagaD.npy │ │ │ ├── bGagaE.npy │ │ │ ├── bHaleB.npy │ │ │ ├── bHaleC.npy │ │ │ ├── bHaleD.npy │ │ │ ├── bNaauB.npy │ │ │ ├── bNaauC.npy │ │ │ ├── bNaauD.npy │ │ │ ├── bOphoC.npy │ │ │ ├── bOphoD.npy │ │ │ ├── bOphoE.npy │ │ │ ├── bPafaB.npy │ │ │ ├── bPafaC.npy │ │ │ ├── bPafaD.npy │ │ │ ├── bPskrB.npy │ │ │ ├── bPskrC.npy │ │ │ ├── bPskrD.npy │ │ │ ├── bPskrE.npy │ │ │ ├── bPyadB.npy │ │ │ ├── bPyadC.npy │ │ │ ├── bPyadD.npy │ │ │ ├── bSecoD.npy │ │ │ ├── bSecoE.npy │ │ │ ├── bStocB.npy │ │ │ ├── bStocC.npy │ │ │ ├── bStocD.npy │ │ │ ├── bStocE.npy │ │ │ ├── bUrpeB.npy │ │ │ ├── bUrpeC.npy │ │ │ ├── bUrpeD.npy │ │ │ ├── cAlmiC.npy │ │ │ ├── cAlmiD1.npy │ │ │ ├── cAlmiD3.npy │ │ │ ├── cAlmiE.npy │ │ │ ├── cAlsiC.npy │ │ │ ├── cAlsiD3.npy │ │ │ ├── cChmyD1.npy │ │ │ ├── cChmyD3.npy │ │ │ ├── cChmyF.npy │ │ │ ├── cChpiD1.npy │ │ │ ├── cChpiD2.npy │ │ │ ├── cChpiD3.npy │ │ │ ├── cChpiF.npy │ │ │ ├── cCrpoC.npy │ │ │ ├── cCrpoD1.npy │ │ │ ├── cCrpoD3.npy │ │ │ ├── cCrpoE.npy │ │ │ ├── cGavganC.npy │ │ │ ├── cGavganD1.npy │ │ │ ├── cGavganD3.npy │ │ │ ├── cGavganE.npy │ │ │ ├── cGoagD1.npy │ │ │ ├── cGoagD2.npy │ │ │ ├── cGoagD3.npy │ │ │ ├── cGoagE.npy │ │ │ ├── cGoagF.npy │ │ │ ├── cPesiD1.npy │ │ │ ├── cPesiD2.npy │ │ │ ├── cPesiD3.npy │ │ │ ├── cPesiE.npy │ │ │ ├── cPesiF.npy │ │ │ ├── mAifuC.npy │ │ │ ├── mAifuD.npy │ │ │ ├── mAifuE.npy │ │ │ ├── mAifuF.npy │ │ │ ├── mAifuV.npy │ │ │ ├── mAimeC.npy │ │ │ ├── mAimeDa.npy │ │ │ ├── mAimeDb.npy │ │ │ ├── mAimeE.npy │ │ │ ├── mAimeF.npy │ │ │ ├── mBibiA2.npy │ │ │ ├── mBibiA3.npy │ │ │ ├── mBibiA4.npy │ │ │ ├── mBibiC.npy │ │ │ ├── mBibiDa.npy │ │ │ ├── mBibiDb.npy │ │ │ ├── mBibiE.npy │ │ │ ├── mBibiF.npy │ │ │ ├── mBotaA.npy │ │ │ ├── mBotaA3.npy │ │ │ ├── mBotaA5.npy │ │ │ ├── mBotaC.npy │ │ │ ├── mBotaDa.npy │ │ │ ├── mBotaDb.npy │ │ │ ├── mBotaF.npy │ │ │ ├── mBotaV.npy │ │ │ ├── mCahiA.npy │ │ │ ├── mCahiA2.npy │ │ │ ├── mCahiA4.npy │ │ │ ├── mCahiA5.npy │ │ │ ├── mCahiC.npy │ │ │ ├── mCahiDa.npy │ │ │ ├── mCahiDb.npy │ │ │ ├── mCahiE.npy │ │ │ ├── mCahiF.npy │ │ │ ├── mCahiV.npy │ │ │ ├── mCaluC.npy │ │ │ ├── mCaluD1.npy │ │ │ ├── mCaluE.npy │ │ │ ├── mCaluF.npy │ │ │ ├── mCaluV.npy │ │ │ ├── mChlaA2.npy │ │ │ ├── mChlaA3.npy │ │ │ ├── mChlaA4.npy │ │ │ ├── mChlaC.npy │ │ │ ├── mChlaD.npy │ │ │ ├── mChlaE.npy │ │ │ ├── mChlaF.npy │ │ │ ├── mChlaV.npy │ │ │ ├── mCocrA2.npy │ │ │ ├── mCocrA3.npy │ │ │ ├── mCocrD.npy │ │ │ ├── mCocrE.npy │ │ │ ├── mCocrF.npy │ │ │ ├── mCocrV.npy │ │ │ ├── mDanoA.npy │ │ │ ├── mDanoC.npy │ │ │ ├── mDanoD.npy │ │ │ ├── mDanoF.npy │ │ │ ├── mDanoV.npy │ │ │ ├── mEledA1.npy │ │ │ ├── mEledA2.npy │ │ │ ├── mEledA3.npy │ │ │ ├── mEledD1.npy │ │ │ ├── mEledE.npy │ │ │ ├── mEledF.npy │ │ │ ├── mEledV.npy │ │ │ ├── mEnluC.npy │ │ │ ├── mEnluD1.npy │ │ │ ├── mEnluE.npy │ │ │ ├── mEnluF.npy │ │ │ ├── mEnluV.npy │ │ │ ├── mEqcaA.npy │ │ │ ├── mEqcaC.npy │ │ │ ├── mEqcaD.npy │ │ │ ├── mEqcaE.npy │ │ │ ├── mEqcaF.npy │ │ │ ├── mEqcaV.npy │ │ │ ├── mEreuA1.npy │ │ │ ├── mEreuA10.npy │ │ │ ├── mEreuA11.npy │ │ │ ├── mEreuA12.npy │ │ │ ├── mEreuA13.npy │ │ │ ├── mEreuA14.npy │ │ │ ├── mEreuA15.npy │ │ │ ├── mEreuA2.npy │ │ │ ├── mEreuA3.npy │ │ │ ├── mEreuA5.npy │ │ │ ├── mEreuA6.npy │ │ │ ├── mEreuA7.npy │ │ │ ├── mEreuA8.npy │ │ │ ├── mEreuA9.npy │ │ │ ├── mEreuC.npy │ │ │ ├── mEreuD1.npy │ │ │ ├── mEreuE.npy │ │ │ ├── mEreuF.npy │ │ │ ├── mEreuV.npy │ │ │ ├── mFecaD.npy │ │ │ ├── mFecaE.npy │ │ │ ├── mFecaF.npy │ │ │ ├── mFecaV.npy │ │ │ ├── mHeglA1.npy │ │ │ ├── mHeglA2.npy │ │ │ ├── mHeglA3.npy │ │ │ ├── mHeglD.npy │ │ │ ├── mHeglE.npy │ │ │ ├── mHeglF.npy │ │ │ ├── mHeglV.npy │ │ │ ├── mHosaA.npy │ │ │ ├── mHosaD.npy │ │ │ ├── mHosaE.npy │ │ │ ├── mHosaF.npy │ │ │ ├── mHosaV.npy │ │ │ ├── mLoafA1.npy │ │ │ ├── mLoafA2.npy │ │ │ ├── mLoafC.npy │ │ │ ├── mLoafD.npy │ │ │ ├── mLoafE.npy │ │ │ ├── mLoafF.npy │ │ │ ├── mLoafV.npy │ │ │ ├── mMamaA1.npy │ │ │ ├── mMamaD.npy │ │ │ ├── mMamaE.npy │ │ │ ├── mMamaF.npy │ │ │ ├── mMamaV.npy │ │ │ ├── mMimuA.npy │ │ │ ├── mMimuC.npy │ │ │ ├── mMimuD.npy │ │ │ ├── mMimuE.npy │ │ │ ├── mMimuF.npy │ │ │ ├── mMimuV.npy │ │ │ ├── mModoC.npy │ │ │ ├── mModoD.npy │ │ │ ├── mModoE.npy │ │ │ ├── mModoF.npy │ │ │ ├── mModoV1.npy │ │ │ ├── mModoV2.npy │ │ │ ├── mMumuA.npy │ │ │ ├── mMumuC.npy │ │ │ ├── mMumuD1.npy │ │ │ ├── mMumuE.npy │ │ │ ├── mMumuF.npy │ │ │ ├── mMumuV1.npy │ │ │ ├── mMupuC.npy │ │ │ ├── mMupuD.npy │ │ │ ├── mMupuE.npy │ │ │ ├── mMupuF.npy │ │ │ ├── mMupuV.npy │ │ │ ├── mMyluA1.npy │ │ │ ├── mMyluA2.npy │ │ │ ├── mMyluA4.npy │ │ │ ├── mMyluC.npy │ │ │ ├── mMyluD.npy │ │ │ ├── mMyluE.npy │ │ │ ├── mMyluF.npy │ │ │ ├── mMyluV.npy │ │ │ ├── mNescD.npy │ │ │ ├── mNescE.npy │ │ │ ├── mNescF.npy │ │ │ ├── mNescV.npy │ │ │ ├── mOcprA1.npy │ │ │ ├── mOcprA2.npy │ │ │ ├── mOcprA3.npy │ │ │ ├── mOcprC.npy │ │ │ ├── mOcprD.npy │ │ │ ├── mOcprE.npy │ │ │ ├── mOcprF.npy │ │ │ ├── mOcprV.npy │ │ │ ├── mOdviA1.npy │ │ │ ├── mOdviA2.npy │ │ │ ├── mOdviA3.npy │ │ │ ├── mOdviC.npy │ │ │ ├── mOdviD.npy │ │ │ ├── mOdviE.npy │ │ │ ├── mOdviF.npy │ │ │ ├── mOdviV.npy │ │ │ ├── mOran2.npy │ │ │ ├── mOran4.npy │ │ │ ├── mOranD.npy │ │ │ ├── mOranE.npy │ │ │ ├── mOranF.npy │ │ │ ├── mOrcuA.npy │ │ │ ├── mOrcuA2.npy │ │ │ ├── mOrcuA3.npy │ │ │ ├── mOrcuA4.npy │ │ │ ├── mOrcuC.npy │ │ │ ├── mOrcuD.npy │ │ │ ├── mOrcuE.npy │ │ │ ├── mOrcuF.npy │ │ │ ├── mOrcuV.npy │ │ │ ├── mOrorC.npy │ │ │ ├── mOrorD.npy │ │ │ ├── mOrorE.npy │ │ │ ├── mOrorV.npy │ │ │ ├── mOvarA1.npy │ │ │ ├── mOvarA2.npy │ │ │ ├── mOvarA3.npy │ │ │ ├── mOvarC.npy │ │ │ ├── mOvarD.npy │ │ │ ├── mOvarF.npy │ │ │ ├── mPahoA1.npy │ │ │ ├── mPahoA3.npy │ │ │ ├── mPahoA5.npy │ │ │ ├── mPahoC.npy │ │ │ ├── mPahoD.npy │ │ │ ├── mPahoE.npy │ │ │ ├── mPahoF.npy │ │ │ ├── mPahoV.npy │ │ │ ├── mPatiC.npy │ │ │ ├── mPatiD.npy │ │ │ ├── mPatiE.npy │ │ │ ├── mPatiF.npy │ │ │ ├── mPatiV.npy │ │ │ ├── mPhciC.npy │ │ │ ├── mPhciDa.npy │ │ │ ├── mPhciDb.npy │ │ │ ├── mPhciE.npy │ │ │ ├── mPhciF.npy │ │ │ ├── mPhciV1.npy │ │ │ ├── mPhciV2.npy │ │ │ ├── mPhciV3.npy │ │ │ ├── mPtvaC.npy │ │ │ ├── mPtvaD.npy │ │ │ ├── mPtvaE.npy │ │ │ ├── mPtvaF.npy │ │ │ ├── mPtvaV.npy │ │ │ ├── mSahaC.npy │ │ │ ├── mSahaD.npy │ │ │ ├── mSahaE.npy │ │ │ ├── mSahaF.npy │ │ │ ├── mSahaV1.npy │ │ │ ├── mSahaV2.npy │ │ │ ├── mSahaV4.npy │ │ │ ├── mSahaV5.npy │ │ │ ├── mSoarA2.npy │ │ │ ├── mSoarA3.npy │ │ │ ├── mSoarC.npy │ │ │ ├── mSoarD.npy │ │ │ ├── mSoarE.npy │ │ │ ├── mSoarF.npy │ │ │ ├── mSoarV.npy │ │ │ ├── mTrmaA2.npy │ │ │ ├── mTrmaC.npy │ │ │ ├── mTrmaD.npy │ │ │ ├── mTrmaE.npy │ │ │ ├── mTrmaF.npy │ │ │ ├── mTrmaV.npy │ │ │ ├── mUrmaC.npy │ │ │ ├── mUrmaD.npy │ │ │ ├── mUrmaV.npy │ │ │ ├── sBocoD.npy │ │ │ ├── sBocoE.npy │ │ │ ├── sBocoF.npy │ │ │ ├── sBocoGo.npy │ │ │ ├── sCradD.npy │ │ │ ├── sCradE.npy │ │ │ ├── sCradF.npy │ │ │ ├── sCradGa.npy │ │ │ ├── sCradGc.npy │ │ │ ├── sCratE.npy │ │ │ ├── sCratF.npy │ │ │ ├── sCratGa.npy │ │ │ ├── sCratGb.npy │ │ │ ├── sCratGc.npy │ │ │ ├── sCratGk49.npy │ │ │ ├── sCrheAE.npy │ │ │ ├── sCrheAF.npy │ │ │ ├── sCrheAGa1.npy │ │ │ ├── sCrheAGa2.npy │ │ │ ├── sCrheAGb.npy │ │ │ ├── sCrheAGc1.npy │ │ │ ├── sCrheBE.npy │ │ │ ├── sCrheBF.npy │ │ │ ├── sCrheBGa1.npy │ │ │ ├── sCrhoAF.npy │ │ │ ├── sCrhoAGa1.npy │ │ │ ├── sCrhoAGa2.npy │ │ │ ├── sCrhoAGb.npy │ │ │ ├── sCrhoAGc1.npy │ │ │ ├── sCrhoBD.npy │ │ │ ├── sCrhoBE.npy │ │ │ ├── sCrhoBF.npy │ │ │ ├── sCrhoBGc1.npy │ │ │ ├── sCrhoGa.npy │ │ │ ├── sCrhoGc.npy │ │ │ ├── sCrscAE.npy │ │ │ ├── sCrscAF.npy │ │ │ ├── sCrscAGa1.npy │ │ │ ├── sCrscAGa2.npy │ │ │ ├── sCrscAGb.npy │ │ │ ├── sCrscAGc1.npy │ │ │ ├── sCrscAGc2.npy │ │ │ ├── sCrscBE.npy │ │ │ ├── sCrscBF.npy │ │ │ ├── sCrscBGa1.npy │ │ │ ├── sCrscBGb.npy │ │ │ ├── sCrscBGc1.npy │ │ │ ├── sCrscBGk49.npy │ │ │ ├── sDeacE.npy │ │ │ ├── sDeacF.npy │ │ │ ├── sDeacGa.npy │ │ │ ├── sDeacGb.npy │ │ │ ├── sDeacGc.npy │ │ │ ├── sDeacGk49.npy │ │ │ ├── sLabiD.npy │ │ │ ├── sLabiE.npy │ │ │ ├── sLabiF.npy │ │ │ ├── sLabiGo.npy │ │ │ ├── sLaviD.npy │ │ │ ├── sLaviE.npy │ │ │ ├── sLaviF.npy │ │ │ ├── sLaviGo.npy │ │ │ ├── sNoscD.npy │ │ │ ├── sNoscE.npy │ │ │ ├── sNoscF.npy │ │ │ ├── sNoscGc.npy │ │ │ ├── sOpgrDb.npy │ │ │ ├── sOpgrF.npy │ │ │ ├── sOpgrG0.npy │ │ │ ├── sOphaD.npy │ │ │ ├── sOphaE.npy │ │ │ ├── sOphaF.npy │ │ │ ├── sOphaGc.npy │ │ │ ├── sPapiE.npy │ │ │ ├── sPapiF.npy │ │ │ ├── sPapiG0.npy │ │ │ ├── sPoviD.npy │ │ │ ├── sPoviE.npy │ │ │ ├── sPoviF.npy │ │ │ ├── sPoviG0.npy │ │ │ ├── sPrflE.npy │ │ │ ├── sPrflGa1.npy │ │ │ ├── sPrflGa2.npy │ │ │ ├── sPrflGb.npy │ │ │ ├── sPrflGck.npy │ │ │ ├── sPrflGk49.npy │ │ │ ├── sPrmuE.npy │ │ │ ├── sPrmuF.npy │ │ │ ├── sPrmuGa1.npy │ │ │ ├── sPrmuGa2.npy │ │ │ ├── sPrmuGb.npy │ │ │ ├── sPrmuGck.npy │ │ │ ├── sPrmuGk49.npy │ │ │ ├── sPsteD.npy │ │ │ ├── sPsteE.npy │ │ │ ├── sPsteF.npy │ │ │ ├── sPsteGc.npy │ │ │ ├── sPybiE.npy │ │ │ ├── sPybiF.npy │ │ │ ├── sVibeEa.npy │ │ │ ├── sVibeF.npy │ │ │ ├── sVibeGa1.npy │ │ │ ├── sVibeGa2.npy │ │ │ └── sVibeGa4.npy │ └── emmaemb_pla2g2.ipynb ├── __init__.py └── deeploc │ ├── deeploc_emma.py │ ├── deeploc_train.fasta │ └── deeploc_train_features.csv ├── images └── emma_overview.jpg ├── plm_embeddings ├── README.md ├── __init__.py ├── ankh_models.py ├── delete_embeddings.py ├── embedding_handler.py ├── embedding_handler_selector.py ├── embedding_model_metadata.json ├── embedding_model_metadata_handler.py ├── esm3.py ├── esm_fair.py ├── get_embeddings.py ├── requirements │ ├── emmaplm_requirements.txt │ └── esm3_requirements.txt ├── t5.py ├── test_embedding_scripts.py └── utils.py └── pyproject.toml /.github/workflows/main.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/broadinstitute/EmmaEmb/HEAD/.github/workflows/main.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/broadinstitute/EmmaEmb/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/broadinstitute/EmmaEmb/HEAD/LICENSE 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