cherryml/__init__.py,sha256=x6pVzttERlMhF1LxG3yf8XrdQXIZxAN6A2LGHHJGxyo,642
cherryml/__main__.py,sha256=1GTCXPnoZ5l4rTHPGyU0XCkjcrKW2YZaho2YbDhUEXk,8523
cherryml/_cherryml_public_api.py,sha256=LvHfhvlQrTHW0kEnvSiS9V8GNioXS2nkep6jdFO9pkk,9176
cherryml/global_vars.py,sha256=6oUkUGHRps2DshFfXcLivNUdhQGFKCJW5PPBSu7vYp4,15
cherryml/types.py,sha256=MGz4vcW3_iHe8Bk5GkLyXJ-6WydKt50f_b368rNJSnw,308
cherryml/utils.py,sha256=BRup4hCgaFLza5yVE4k_y-Qx_otCQn9fLeEAyIOWSIg,2102
cherryml/_siterm/fast_site_rates.cpp,sha256=88k5Idmqem4YRGaObbcTmGLUoM4sCleX3lSSNF9gb88,1174932
cherryml/benchmarking/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
cherryml/benchmarking/globals.py,sha256=UNBr67gCiUW-U-3NWBOM9p7FgB0PaxHHRGhcfrbilIU,34
cherryml/benchmarking/lg_paper.py,sha256=9IiLi26GWV7d9bdGIwcoKzz2nhJPD_9LkDC42Ry5dmg,20636
cherryml/benchmarking/pfam_15k.py,sha256=CnkKROOJkeZ6Le5il8gvaMZAmRk2hcx3zWcRhvSmDZQ,19172
cherryml/benchmarking/_contact_generation/ContactMatrix.py,sha256=94Oolx6PXl1jlmCCGRW-bAJQVUH0Wh6wE8zoxr-mCJo,2538
cherryml/benchmarking/_contact_generation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
cherryml/caching/__init__.py,sha256=G7HlKAc3olzJbk8ARccoPZPZDe0rZqNg2gOpOKtefnU,701
cherryml/caching/_cached.py,sha256=3A55zlwfxg7qYpAVAmtp9f3YwV32q_Re1mXIJFHlsQo,7152
cherryml/caching/_cached_computation.py,sha256=01wVgE6-Xfm74PFp4fCv-oy0i0tDpSh9M7WLqQ8_lE4,13846
cherryml/caching/_cached_parallel_computation.py,sha256=dhOS_QgwtQWzZoYQxAJy1CQhum0cPJHb3NtGhpvLd9s,17493
cherryml/caching/_common.py,sha256=Bs6Q4U71pc3AXBGHry1eSlzRorLmoJRXm30jBYQXjnE,5289
cherryml/counting/__init__.py,sha256=9OBjZdtayPYw6u9lVBk4DFavMM2y-8PgQRUt5yyFfgA,106
cherryml/counting/_count_co_transitions.cpp,sha256=Bq2xfQatfxz1j6_kxE0y55EMQ2mkHi9BHJx336-L5QA,31873
cherryml/counting/_count_co_transitions.py,sha256=DKxqcGy8gPhovL0c6vD3uYlLJtPDWbpo2TOZXlMK7Rc,17250
cherryml/counting/_count_transitions.cpp,sha256=WRfYDlybjcNBUUsHkgkcDF5gNd2fZB5OEC-OmAnPNnA,26997
cherryml/counting/_count_transitions.py,sha256=RArpwZpz9jTBWoXqBYNDi5ZIIZEUj5oi-ZEbJCcAIsI,15615
cherryml/estimation/__init__.py,sha256=JiGjB0nUYE_MXdVxoT6jngdGqkcV2ct0vktYlIZaal4,160
cherryml/estimation/_em_lg.py,sha256=k_pUnu0bvgqkNz3hGSKvX32EMvUgOi1PSbrXkQW_1Vk,11124
cherryml/estimation/_em_lg_xrate.py,sha256=-oQMkcCOfyYjqKIe_xmLd-iWckU077w9sBBLFHcWGB8,11327
cherryml/estimation/_jtt_ipw.py,sha256=ZtTlZ2a9WERkLakIpCvf39etE9i03wYz6noGdX7qsjs,3701
cherryml/estimation/_quantized_transitions_mle.py,sha256=fDJjYtW9hQW4aR7YtkmVg-j0-7z7JJCWFQ5lE_PywJQ,4191
cherryml/estimation/_ratelearn/__init__.py,sha256=8QN-ca9gJ8WbPO8ubMu6h0Gai1o70XVLHPemSm3H23U,502
cherryml/estimation/_ratelearn/rate.py,sha256=6jv612lKzJeUK_qXT4uHVHQsQTyuU86AJTO2Z4dmujc,7777
cherryml/estimation/_ratelearn/ratelearner.py,sha256=O4kiRUDX-Gzw5Af9E55vYyXoIG_lutRwr9BIVlw2OHg,5813
cherryml/estimation/_ratelearn/simulate.py,sha256=HosGFg1lmbtIIsFQyYdPWqxBvkkSsFN8_aI74UM_lJs,6150
cherryml/estimation/_ratelearn/trainer.py,sha256=s-4sTeujOVvdg0Btb3hqAFs5RLmzvWwnarBiHzuILRg,13740
cherryml/estimation/historian/src/ECMrest.cpp,sha256=NGyQj80qyNk00AMe5zykZbPWEhJm4L4pCOpyJbhog8M,23688
cherryml/estimation/historian/src/ECMunrest.cpp,sha256=wwVTpnSMTE--ghON8hR3R9guxVxzPeu5mql6oTK1k9E,144197
cherryml/estimation/historian/src/alignpath.cpp,sha256=f4GkCmX4DO0IWijCzDYlv-GojR5U5OvF3VZ4pxLSrEo,10397
cherryml/estimation/historian/src/ctok.cpp,sha256=T_fpj3-PixLMe_pTxlMoIoOTlO9ux-PoFo4Ow7q7VHs,5554
cherryml/estimation/historian/src/dayhoff.cpp,sha256=1RYuYOKvWNXUbHvTlclkgOBBQA-u7zpTN2xpajNhYK4,13498
cherryml/estimation/historian/src/diagenv.cpp,sha256=WfMs2KUSbZBMdq6buccEPfeCVrGoSqt1N30OVGaqmaA,8539
cherryml/estimation/historian/src/fastseq.cpp,sha256=NruT5Z7K75HEgpDoo0Sp7G7z5MaZ5qIoCQV4397WBls,7750
cherryml/estimation/historian/src/forward.cpp,sha256=j6GbkrCvxVoTTFgulyfsVc7tS9ZChGyVooxS9XgJZdo,50475
cherryml/estimation/historian/src/gamma.cpp,sha256=hkc_bT2GwyGrra8SCX8htaAihAw7VilavTE1xxXLuIo,1152
cherryml/estimation/historian/src/gason.cpp,sha256=14WGLoVwZJOq5JKzR7dd8BOXxN7oAeEBfG1basbZr6w,9479
cherryml/estimation/historian/src/jc.cpp,sha256=8XnxTEDidpTHccY3clINZLuybSc4yBNoLNW6tUcLSog,643
cherryml/estimation/historian/src/jcrna.cpp,sha256=uIunIMDbneVrMYEg5lkux7OBJ2TEaOFzxeRblDeBm_s,655
cherryml/estimation/historian/src/jones.cpp,sha256=W25fcOWWJ0NscOflg0iY-r6pN7vgW8s3p-VhkiyVTtg,16139
cherryml/estimation/historian/src/jsonutil.cpp,sha256=A0PvY92ZlpPEAhDSoKDIYCCnlQ83eJwtwUWqSqqc7F8,4833
cherryml/estimation/historian/src/knhx.cpp,sha256=RqNajczCuyaMFRLyp61lkrxZNud1c5rI8n-HFGAoDuI,4451
cherryml/estimation/historian/src/lg.cpp,sha256=F94MJISAxgCTocCOk-197t7nbvDSEKt1LHigbLfkp6E,16145
cherryml/estimation/historian/src/logger.cpp,sha256=k209tEPoBOSMoOPv_GnHH0pEX-JCRrAmJJxlQEVR8dM,4318
cherryml/estimation/historian/src/logsumexp.cpp,sha256=4R5MQlcxC6h6vqVINir_pcrg-9FOiEB6CY4oIMml220,3435
cherryml/estimation/historian/src/memsize.cpp,sha256=aMHxqlwCaWjewSXTzV5nW8Bk8KYQaGxegyzcfbB7vKQ,3152
cherryml/estimation/historian/src/model.cpp,sha256=jgS1PeFPyEn9Gh3fJfVpVqq91Qf02Yo0G1sgSQpQAYQ,49882
cherryml/estimation/historian/src/nexus.cpp,sha256=svUW1LMk-CtHV0ewLKcm_ZeTBVqo96YYIVAd2H08PqY,3731
cherryml/estimation/historian/src/optparser.cpp,sha256=kKTasbCOp2h1pAxYT95y6Ifdql5ShqvdU3ZRIQMnM1U,1991
cherryml/estimation/historian/src/pairhmm.cpp,sha256=dt4uUMDzCWOTko-TkE5WwXusgwO9UyqCAXS47ZcD4nc,3956
cherryml/estimation/historian/src/presets.cpp,sha256=RSF4icZrWP76p3J1wpT7KvsTl6L7Dn-hgKQkhvdLvK0,762
cherryml/estimation/historian/src/profile.cpp,sha256=QFjhcZZZbZyjzhmPKPSJ2CJ8QUI9kNfAiE-7ZH1RPq8,13215
cherryml/estimation/historian/src/quickalign.cpp,sha256=euYvJW8i6YZQnGOh9Lcn5VD3s1FHiQisnTrwvjMmEwg,6642
cherryml/estimation/historian/src/recon.cpp,sha256=NexqaxGQ4c9qKnkNPBF41xly3cHQp2vRGvNByBQDGJQ,53182
cherryml/estimation/historian/src/refiner.cpp,sha256=oGbxy8PiAr2IVmQFAaTcRgVFgefmlEZXmE3uDyaKMGI,7750
cherryml/estimation/historian/src/sampler.cpp,sha256=zMP9N0NMtwgDIB2rHHTwFMIL1PXBNGtpQgqse2VbLwY,74794
cherryml/estimation/historian/src/seqgraph.cpp,sha256=XcvHG47IPRilhEv-BmI8xaGenCYdQmUjnI2hDt7-zWQ,8089
cherryml/estimation/historian/src/simulator.cpp,sha256=zAbVKFO0CUspLGUdB69euU-UDr1K6ZfKG3EIhkYmWrc,6698
cherryml/estimation/historian/src/span.cpp,sha256=S1FPJBdnvcCHyvI_iGfaTHet3KbEbRESJ915es98E9Q,5011
cherryml/estimation/historian/src/stockholm.cpp,sha256=jIlUA4RBBd6qN9BicXnRufq-fTK-QpizBUdi52KkuWU,6214
cherryml/estimation/historian/src/sumprod.cpp,sha256=8ZOt-2kOCzlHXdPk_LQlS44ME3VIJYNmai4F9Qmfdb4,17068
cherryml/estimation/historian/src/tree.cpp,sha256=cgSYUeqaZb7Ufzlnv1_nudgkAoW0G32AEE5Mt9f-MSM,25022
cherryml/estimation/historian/src/util.cpp,sha256=RGRenu19j0Jl4spQDdosWjBCP99QJH7k3Ej1QIT04NE,2365
cherryml/estimation/historian/src/wag.cpp,sha256=VkHJoBiwH-9i0MGbkkh-Z9YDv57A6893sMf6f6BNfjE,16124
cherryml/estimation/historian/t/testaligncount.cpp,sha256=_EE45_CrQLx2TLNfKPaYZuHL1sG4xWTCqPRtV-yHxQI,1695
cherryml/estimation/historian/t/testbackward.cpp,sha256=DftVAvPNAMxRpMBgEMpU54Tcmc3qlZwdCvZN8ANGE4g,1303
cherryml/estimation/historian/t/testcountio.cpp,sha256=aZW2bd3XdReW2UT05kQkkAfcNfXa6ZPHBHs0QWIY_oU,388
cherryml/estimation/historian/t/testforward.cpp,sha256=o2pph2iEBtLyXSCVzCUxajCW4PeexQMww7GHztpDiIU,2227
cherryml/estimation/historian/t/testlogsumexp.cpp,sha256=fSjndhsrxRJADnt9oEKVqlqMKDQX117FU4t6fXKo5mA,670
cherryml/estimation/historian/t/testmatexp.cpp,sha256=aOg_NTx_P0WoqTDjy-wMO3U8fwppHSa9erRNKOJ4qDo,813
cherryml/estimation/historian/t/testmerge.cpp,sha256=l2YqOwAda_6a8p4NFP2PLsSAziCWc__PPwLoGUKSwZg,934
cherryml/estimation/historian/t/testnexus.cpp,sha256=7WLDQ9cR7bY8HaQSyOHltjNzZuIAUun2WjJLdFiW4Po,330
cherryml/estimation/historian/t/testnj.cpp,sha256=BzbT2_6ogMR3IjKTy7HAKAb8Z0GRbUv9MahoYdgEcXM,663
cherryml/estimation/historian/t/testnullforward.cpp,sha256=uly3PJrA1L8Buc-R84Gnvd4Hu9SZuZDLtTcJg-YzkNQ,1491
cherryml/estimation/historian/t/testnumsubcount.cpp,sha256=8zc87kZeYmX37Kb-fiS347DPwxYC7T8R801kPYjB_NI,2809
cherryml/estimation/historian/t/testquickalign.cpp,sha256=8NWxoLtoxLhY2hKNl68HCDtNi03lU-2GSXdBamO_XqQ,843
cherryml/estimation/historian/t/testrateio.cpp,sha256=XNVyWcJOK2fO-Espu3G58Q3MtIt6HwMyKeHcq35Sqtc,394
cherryml/estimation/historian/t/testregex.cpp,sha256=odYbu0X2dMp0sHeCUZRoNORgecSHVwIzaXFcoYPa_1g,1616
cherryml/estimation/historian/t/testseqio.cpp,sha256=xpjUaZvUkOJ4A-IlDtABhDqJHyqTeFev_FLvwtEO29Y,340
cherryml/estimation/historian/t/testseqprofile.cpp,sha256=K9Uz4XEra_CjDuqwdDw0vd4VgfCx1sGt7L_YS_3Jng0,398
cherryml/estimation/historian/t/testspan.cpp,sha256=PnHCUAjXapTtFmPR_tJRDxHF591dox03Mpi7nNfoBZc,868
cherryml/estimation/historian/t/teststockholm.cpp,sha256=f_GRBbGrYHMtWfyuRZcnS7dHIHWG3dYu2MsFVSdwWtA,338
cherryml/estimation/historian/t/testsubcount.cpp,sha256=DCfcu_eoKqdOWBCGhWpN0sxfxfpl43bf0wqU7WYWzFE,1582
cherryml/estimation/historian/t/testsumprod.cpp,sha256=Mm0hZytVap7irxm3oJAsrRbO6wP2__cP9UeCfhoId9U,1623
cherryml/estimation/historian/t/testtreeio.cpp,sha256=G5wj3Y0BFL2C_h_l3Zi3ZtSDXcg8cvCJa4LNAuva4xg,511
cherryml/estimation/historian/t/testupgma.cpp,sha256=r6TYZbQdO6JYJJI8-j4VMQTAO2jPPPtMAwf65WYmQ8I,653
cherryml/estimation/historian/target/historian.cpp,sha256=UtwqN8F5CbnaKJv_wx359caZHWRpfyVrWceGgQ4jKuk,16956
cherryml/estimation_end_to_end/__init__.py,sha256=CIa9ocC_1w2lg-EyLLbk8X3lCgtjqvDwkAN2iL1n8gg,188
cherryml/estimation_end_to_end/_cherry.py,sha256=HAtv_tZN3P7LOmZxG4LLvBGXq7EXkz26S0DCTvCNszI,18582
cherryml/estimation_end_to_end/_em.py,sha256=1-ojMAtlPHpOgP0yOiOwepOJs7cGxhXfe53B7BvWEHI,7245
cherryml/evaluation/__init__.py,sha256=26y8L7ZYbiFiIRRQETc8QuhBJSCW8Yls2HXJrl03t2Y,360
cherryml/evaluation/__main__.py,sha256=ekhpSqgzgNe2S4Jgg3BCG5XNHx6GyIi2VYvCHu29dW4,2685
cherryml/evaluation/_evaluation_public_api.py,sha256=hsv_wHY3DkHPJHR4-7siU_XsM7z8IF3nI1ZeFvK6i24,5268
cherryml/evaluation/_likelihood.py,sha256=JmbYAXssDrKsCPwmKZlESLSCqtqegCj4Sk3846YMEMM,24215
cherryml/evaluation/_maximal_matching.py,sha256=EMyZbJXcVhETM1G0YUb2WOUcb19YvLmPiz-yXsYhzgo,2977
cherryml/evaluation/_metrics.py,sha256=PpRwqeFsRKA0e0-g5khwqnx3M6QCz_1Q8sNILFdtYOE,7161
cherryml/io/__init__.py,sha256=kM4D_HFY_pHuFZYpfnhH4JM7zKRJ3oXo0JFe5hMYRJ0,717
cherryml/io/_contact_map.py,sha256=7PAbYPK8NIlCAjQETqlAahSQAwVTiOYTkPNfgc6D2uc,1315
cherryml/io/_count_matrices.py,sha256=iF-1W390hg2ZTRTWAAu66dRPzKDYWkgmu0I8gRzbw04,2942
cherryml/io/_log_likelihood.py,sha256=xKA98KbNLup8B2OGm2r8Gnz66fWVYmkPGdC9iPQ0cQo,1460
cherryml/io/_msa.py,sha256=eM4KNtyeGYSf1HsIg_VUnjAxDgpstrywl53dYDImDag,2164
cherryml/io/_pickle.py,sha256=_SCN3cAQL46VfkhkL1wY5IFVeDmulTMra-JNvkuUiDg,314
cherryml/io/_rate_matrix.py,sha256=gpscFBMjO9ZsH64moydr75pPoFUaxnkFCpIBVE9F15M,2676
cherryml/io/_site_rates.py,sha256=3uWS7X8-OmPTJChLdSLlbOPJtgZs939YA7G7pvTz2A8,1261
cherryml/io/_sites_subset.py,sha256=MIsCbxn11EvlMwE372Cx0t6q4LiyxyVhshO4gXdtc_Y,1427
cherryml/io/_tree.py,sha256=l10vwECMuvn1y5bmtV7EcQ0hdiQnyVaCsQkGJzSZWec,8193
cherryml/markov_chain/__init__.py,sha256=WwzcFXxIf2wLuPEM0IwyRVU_0LYIceFpE-QzNM6MWK0,603
cherryml/markov_chain/_markov_chain.py,sha256=AKYboWf6SNzpavu0cTGJrg1jykf6FJZTeGA55xrq-9o,8620
cherryml/phylogeny_estimation/__init__.py,sha256=q_WyksMMdRFwjB3IBBOD_sNQCaWCnuO4quH3p4A6XjY,110
cherryml/phylogeny_estimation/_common.py,sha256=B0pqD5zU3y-TN--xiMeeVr3aw1cXJE025XrSwaF73dU,1305
cherryml/phylogeny_estimation/_fast_tree.py,sha256=BF38MUFm3LNKYRAT1F4zKNVxO7LNMgE8hOBbsV5vsvY,12805
cherryml/phylogeny_estimation/_gt_tree_estimator.py,sha256=xDnoTvbybX70Ea2Mhem5C1nG8oN-OQBan_vZ6y_9Vfw,3382
cherryml/phylogeny_estimation/_phyml.py,sha256=73oDivIGbmt7mmo5rkuoGpKkCo0-SCc506egtEArzQg,10521
cherryml/simulation/__init__.py,sha256=e6AD8YRUHukor_zXBU0awoax45N1Og0ZnnGq8lIBexA,42
cherryml/simulation/_simulate_msas.py,sha256=Ls_LPbLNRchVIs-XCTE3_jgYZONUJr4c5vz9_jlDZdU,16444
cherryml/simulation/simulate.cpp,sha256=mQtITN_liTHXcHzNnRE03iOcIaYb-f27KAMkaGB3HGI,34507
tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
tests/utils.py,sha256=0C68sryKrP1tFSCe2_05uqUutWLEYjZNTKHt2EEKE2o,943
cherryml-0.1.3.dist-info/LICENSE,sha256=2_ejILbTeEWKLz8Vkaoz9QFZN51StpZTqFkB64NlIoA,1522
cherryml-0.1.3.dist-info/METADATA,sha256=Z58P2VD8Yv82hUcrak_rgh1cDvuAMkhAnPvriWwsotQ,482
cherryml-0.1.3.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
cherryml-0.1.3.dist-info/top_level.txt,sha256=DGCmPNoRk4MMXKak6usdLedslmgE19jFAMB_4XqOSy0,15
cherryml-0.1.3.dist-info/RECORD,,
