Added introduction.rst and more documentation.

data/BLAT_jet.res

-AA	pos	chain	axs	cv	pc	tr	freq	trace	clusters	clusnumber	ssjetormax
-MET	1	A	1.0	0.1798	0.6606	0.0	0.0	0.0	0.0	0.0	0.0
-SER	2	A	1.0	0.4007	0.3574	0.0	0.0	0.0	0.0	0.0	0.0
-ILE	3	A	1.0	0.4642	0.638	0.0	0.0	0.0	0.0	0.0	0.0
-GLN	4	A	1.0	0.5616	0.4343	0.0971	0.18	0.0174	0.0	0.0	0.0174
-HIS	5	A	1.0	0.6781	0.5972	0.1113	0.06	0.0066	0.0	0.0	0.0066
-PHE	6	A	1.0	0.645	1.0	0.0928	0.12	0.0111	0.0	0.0	0.0111
-ARG	7	A	1.0	0.6488	0.5067	0.1249	0.34	0.0424	0.0	0.0	0.0424
-VAL	8	A	1.0	0.7859	0.5656	0.1094	0.54	0.059	0.0	0.0	0.059
-ALA	9	A	1.0	0.8354	0.3846	0.1142	0.52	0.0594	0.0	0.0	0.0594
-LEU	10	A	1.0	0.7349	0.7058	0.1591	0.14	0.0222	0.0	0.0	0.0222
-ILE	11	A	1.0	0.7358	0.638	0.1536	0.4	0.0614	0.0	0.0	0.0614
-PRO	12	A	1.0	0.7525	0.466	0.1143	0.38	0.0434	0.0	0.0	0.0434
-PHE	13	A	1.0	0.7142	1.0	0.1342	0.78	0.1047	0.0	0.0	0.1047
-PHE	14	A	1.0	0.686	1.0	0.1743	0.3	0.0522	0.0	0.0	0.0522
-ALA	15	A	1.0	0.8723	0.3846	0.21	0.7	0.147	0.0	0.0	0.147
-ALA	16	A	1.0	0.8165	0.3846	0.3606	0.34	0.1226	0.0	0.0	0.1226
-PHE	17	A	1.0	0.7198	1.0	0.2187	0.76	0.1662	0.0	0.0	0.1662
-CYS	18	A	1.0	0.7581	0.6425	0.2452	0.7	0.1716	0.0	0.0	0.1716
-LEU	19	A	1.0	0.7318	0.7058	0.2104	0.94	0.1978	0.0	0.0	0.1978
-PRO	20	A	1.0	0.6357	0.466	0.2601	0.74	0.1925	0.0	0.0	0.1925
-VAL	21	A	1.0	0.6017	0.5656	0.2712	0.54	0.1464	0.0	0.0	0.1464
-PHE	22	A	1.0	0.491	1.0	0.2798	0.52	0.1455	0.0	0.0	0.1455
-ALA	23	A	1.0	0.4599	0.3846	0.3037	0.92	0.2794	0.0	0.0	0.2794
-HIS	24	A	1.0	0.4471	0.5972	0.2954	0.68	0.2009	0.0	0.0	0.2009
-PRO	25	A	1.0	0.4918	0.466	0.2696	0.9	0.2426	0.0	0.0	0.2426
-GLU	26	A	1.0	0.4252	0.3348	0.3842	0.66	0.2536	0.0	0.0	0.38
-THR	27	A	1.0	0.5993	0.3257	0.5596	1.0	0.5596	0.0	0.0	0.5794
-LEU	28	A	1.0	0.5513	0.7058	0.3062	0.86	0.2633	0.0	0.0	0.6285
-VAL	29	A	1.0	0.443	0.5656	0.2447	0.82	0.2006	0.0	0.0	0.5043
-LYS	30	A	1.0	0.5102	0.2488	0.3921	0.9	0.3528	0.0	0.0	0.4315
-VAL	31	A	0.5	0.6384	0.5656	0.6009	0.98	0.5889	0.0	0.0	0.6136
-LYS	32	A	1.0	0.4541	0.2488	0.4482	0.88	0.3944	0.0	0.0	0.4242
-ASP	33	A	1.0	0.4253	0.3212	0.4874	0.72	0.3509	0.0	0.0	0.3881
-ALA	34	A	0.8	0.5623	0.3846	0.6821	1.0	0.6821	0.0	0.0	0.6222
-GLU	35	A	1.0	0.4961	0.3348	0.7952	1.0	0.7952	0.0	0.0	0.6457
-ASP	36	A	1.0	0.3478	0.3212	0.3964	0.82	0.325	0.0	0.0	0.3364
-GLN	37	A	1.0	0.357	0.4343	0.3527	0.92	0.3244	0.0	0.0	0.3956
-LEU	38	A	0.8	0.5159	0.7058	0.5341	1.0	0.5341	0.0	0.0	0.62
-GLY	39	A	1.0	0.3705	0.4117	0.6772	0.94	0.6365	0.0	0.0	0.5241
-ALA	40	A	1.0	0.489	0.3846	0.8016	1.0	0.8016	0.0	0.0	0.6453
-ARG	41	A	1.0	0.5109	0.5067	0.7641	1.0	0.7641	0.0	0.0	0.6375
-VAL	42	A	0.8	0.6763	0.5656	0.7475	1.0	0.7475	0.0	0.0	0.7119
-GLY	43	A	0.5	0.7337	0.4117	0.8915	1.0	0.8915	0.0	0.0	0.8126
-TYR	44	A	0.5	0.7363	0.7963	0.7625	1.0	0.7625	0.0	0.0	0.7794
-ILE	45	A	0.8	0.7024	0.638	0.557	0.98	0.5459	0.0	0.0	0.6702
-GLU	46	A	1.0	0.6608	0.3348	0.6645	1.0	0.6645	0.0	0.0	0.6626
-LEU	47	A	0.8	0.6131	0.7058	0.5707	1.0	0.5707	0.0	0.0	0.6594
-ASP	48	A	1.0	0.4773	0.3212	0.6963	1.0	0.6963	0.0	0.0	0.5868
-LEU	49	A	1.0	0.5763	0.7058	0.6209	1.0	0.6209	0.0	0.0	0.6634
-ASN	50	A	1.0	0.3649	0.3936	0.4828	0.96	0.4635	0.0	0.0	0.4286
-SER	51	A	1.0	0.3455	0.3574	0.4897	0.96	0.4702	0.0	0.0	0.4138
-GLY	52	A	1.0	0.4463	0.4117	0.7399	0.98	0.7251	0.0	0.0	0.5857
-LYS	53	A	1.0	0.3604	0.2488	0.3841	0.94	0.3611	0.0	0.0	0.3608
-ILE	54	A	1.0	0.4851	0.638	0.3776	0.92	0.3473	0.0	0.0	0.5616
-LEU	55	A	1.0	0.4936	0.7058	0.4812	0.98	0.4716	0.0	0.0	0.5997
-GLU	56	A	1.0	0.558	0.3348	0.2356	0.54	0.1272	0.0	0.0	0.4464
-SER	57	A	1.0	0.5527	0.3574	0.4512	0.86	0.388	0.0	0.0	0.4704
-PHE	58	A	1.0	0.5465	1.0	0.4883	1.0	0.4883	0.0	0.0	0.7732
-ARG	59	A	1.0	0.4849	0.5067	0.7882	1.0	0.7882	0.0	0.0	0.6475
-PRO	60	A	1.0	0.5275	0.466	0.5851	0.98	0.5734	0.0	0.0	0.5504
-GLU	61	A	1.0	0.4332	0.3348	0.5789	0.96	0.5557	0.0	0.0	0.4944
-GLU	62	A	1.0	0.4866	0.3348	0.772	1.0	0.772	0.0	0.0	0.6293
-ARG	63	A	1.0	0.5151	0.5067	0.7803	1.0	0.7803	0.0	0.0	0.6477
-PHE	64	A	0.8	0.699	1.0	0.8392	1.0	0.8392	0.0	0.0	0.9196
-PRO	65	A	0.8	0.7157	0.466	0.7796	1.0	0.7796	0.0	0.0	0.7476
-MET	66	A	0.8	0.8332	0.6606	0.7335	1.0	0.7335	0.0	0.0	0.7834
-MET	67	A	0.8	0.8131	0.6606	0.7926	1.0	0.7926	0.0	0.0	0.8029
-SER	68	A	1.0	0.8463	0.3574	0.9572	1.0	0.9572	0.6355	1.0	0.9018
-THR	69	A	0.5	0.9843	0.3257	0.8622	1.0	0.8622	0.0	0.0	0.9232
-PHE	70	A	0.8	0.8894	1.0	0.7921	1.0	0.7921	0.0	0.0	0.9447
-LYS	71	A	0.5	0.8959	0.2488	0.9589	1.0	0.9589	0.0	0.0	0.9274
-VAL	72	A	0.5	0.9561	0.5656	0.6351	1.0	0.6351	0.0	0.0	0.7956
-LEU	73	A	0.8	0.8761	0.7058	0.7186	1.0	0.7186	0.0	0.0	0.7974
-LEU	74	A	0.5	0.858	0.7058	0.7184	1.0	0.7184	0.0	0.0	0.7882
-CYS	75	A	0.5	0.8582	0.6425	0.7897	1.0	0.7897	0.0	0.0	0.824
-GLY	76	A	0.5	0.7779	0.4117	0.6851	1.0	0.6851	0.0	0.0	0.7315
-ALA	77	A	0.8	0.6935	0.3846	0.693	1.0	0.693	0.0	0.0	0.6932
-VAL	78	A	0.5	0.7046	0.5656	0.6326	1.0	0.6326	0.0	0.0	0.6686
-LEU	79	A	0.8	0.6453	0.7058	0.9168	1.0	0.9168	0.0	0.0	0.8113
-SER	80	A	1.0	0.5395	0.3574	0.5117	0.98	0.5015	0.0	0.0	0.5205
-ARG	81	A	1.0	0.4735	0.5067	0.6856	1.0	0.6856	0.0	0.0	0.5962
-VAL	82	A	1.0	0.4813	0.5656	0.7089	1.0	0.7089	0.0	0.0	0.6372
-ASP	83	A	1.0	0.4098	0.3212	0.8243	1.0	0.8243	0.0	0.0	0.617
-ALA	84	A	1.0	0.3341	0.3846	0.371	1.0	0.371	0.0	0.0	0.3778
-GLY	85	A	1.0	0.2913	0.4117	0.833	1.0	0.833	0.0	0.0	0.6224
-GLN	86	A	1.0	0.3254	0.4343	0.3336	0.96	0.3202	0.0	0.0	0.3798
-GLU	87	A	0.8	0.4682	0.3348	0.7056	1.0	0.7056	0.0	0.0	0.5869
-GLN	88	A	1.0	0.3582	0.4343	0.4124	1.0	0.4124	0.0	0.0	0.4234
-LEU	89	A	1.0	0.5127	0.7058	0.8865	1.0	0.8865	0.0	0.0	0.7961
-GLY	90	A	1.0	0.3832	0.4117	0.5267	0.9	0.4741	0.0	0.0	0.4429
-ARG	91	A	1.0	0.416	0.5067	0.6849	1.0	0.6849	0.0	0.0	0.5958
-ARG	92	A	1.0	0.3542	0.5067	0.6188	1.0	0.6188	0.0	0.0	0.5628
-ILE	93	A	1.0	0.5106	0.638	0.5855	0.98	0.5738	0.0	0.0	0.6059
-HIS	94	A	1.0	0.3345	0.5972	0.3589	0.8	0.2871	0.0	0.0	0.4658
-TYR	95	A	1.0	0.4788	0.7963	0.5885	1.0	0.5885	0.0	0.0	0.6924
-SER	96	A	1.0	0.3264	0.3574	0.3839	1.0	0.3839	0.0	0.0	0.3707
-GLN	97	A	1.0	0.2683	0.4343	0.3573	0.92	0.3287	0.0	0.0	0.3815
-ASN	98	A	1.0	0.2567	0.3936	0.3483	0.94	0.3274	0.0	0.0	0.3605
-ASP	99	A	1.0	0.4286	0.3212	0.7201	1.0	0.7201	0.0	0.0	0.5743
-LEU	100	A	1.0	0.4296	0.7058	0.7247	1.0	0.7247	0.6192	1.0	0.7152
-VAL	101	A	1.0	0.5086	0.5656	0.6393	1.0	0.6393	0.0	0.0	0.6024
-GLU	102	A	1.0	0.4648	0.3348	0.413	0.86	0.3552	0.0	0.0	0.41
-TYR	103	A	1.0	0.5424	0.7963	0.6543	1.0	0.6543	0.6695	1.0	0.7253
-SER	104	A	1.0	0.5235	0.3574	0.7693	1.0	0.7693	0.564	1.0	0.6464
-PRO	105	A	1.0	0.4902	0.466	0.8633	1.0	0.8633	0.6236	1.0	0.6768
-VAL	106	A	1.0	0.5153	0.5656	0.6077	1.0	0.6077	0.0	0.0	0.5866
-THR	107	A	0.5	0.5797	0.3257	0.7372	1.0	0.7372	0.0	0.0	0.6584
-GLU	108	A	1.0	0.3832	0.3348	0.5514	1.0	0.5514	0.0	0.0	0.4673
-LYS	109	A	1.0	0.33	0.2488	0.472	1.0	0.472	0.0	0.0	0.401
-HIS	110	A	1.0	0.4044	0.5972	0.597	1.0	0.597	0.0	0.0	0.5971
-LEU	111	A	1.0	0.3431	0.7058	0.5623	1.0	0.5623	0.0	0.0	0.634
-THR	112	A	1.0	0.2267	0.3257	0.6024	1.0	0.6024	0.0	0.0	0.464
-ASP	113	A	1.0	0.296	0.3212	0.4415	1.0	0.4415	0.0	0.0	0.3813
-GLY	114	A	0.8	0.4171	0.4117	0.7344	1.0	0.7344	0.0	0.0	0.5758
-MET	115	A	0.8	0.5403	0.6606	0.668	1.0	0.668	0.0	0.0	0.6643
-THR	116	A	1.0	0.4768	0.3257	0.6601	1.0	0.6601	0.0	0.0	0.5684
-VAL	117	A	0.5	0.6126	0.5656	0.5921	1.0	0.5921	0.0	0.0	0.6023
-ARG	118	A	1.0	0.4881	0.5067	0.4469	1.0	0.4469	0.0	0.0	0.4974
-GLU	119	A	1.0	0.5229	0.3348	0.6054	1.0	0.6054	0.0	0.0	0.5642
-LEU	120	A	0.5	0.7037	0.7058	0.8074	1.0	0.8074	0.0	0.0	0.7566
-CYS	121	A	0.5	0.7749	0.6425	0.8041	1.0	0.8041	0.0	0.0	0.7895
-SER	122	A	1.0	0.6332	0.3574	0.5345	0.98	0.5238	0.0	0.0	0.5785
-ALA	123	A	0.8	0.6798	0.3846	0.8645	1.0	0.8645	0.0	0.0	0.7722
-ALA	124	A	0.5	0.8333	0.3846	0.7104	1.0	0.7104	0.0	0.0	0.7718
-ILE	125	A	0.5	0.815	0.638	0.6368	1.0	0.6368	0.0	0.0	0.7265
-THR	126	A	1.0	0.6349	0.3257	0.667	1.0	0.667	0.0	0.0	0.651
-MET	127	A	1.0	0.5665	0.6606	0.5067	0.98	0.4966	0.0	0.0	0.6136
-SER	128	A	1.0	0.7294	0.3574	0.9486	1.0	0.9486	0.6312	1.0	0.839
-ASP	129	A	0.5	0.694	0.3212	0.9405	1.0	0.9405	0.0	0.0	0.8172
-ASN	130	A	1.0	0.674	0.3936	0.8905	1.0	0.8905	0.6312	1.0	0.7822
-THR	131	A	0.8	0.6281	0.3257	0.6701	1.0	0.6701	0.0	0.0	0.6491
-ALA	132	A	0.5	0.7599	0.3846	0.902	1.0	0.902	0.0	0.0	0.831
-ALA	133	A	0.5	0.8236	0.3846	0.7275	1.0	0.7275	0.0	0.0	0.7756
-ASN	134	A	1.0	0.6487	0.3936	0.9255	1.0	0.9255	0.6217	1.0	0.7871
-LEU	135	A	1.0	0.6292	0.7058	0.7598	1.0	0.7598	0.0	0.0	0.7328
-LEU	136	A	0.5	0.7834	0.7058	0.8068	1.0	0.8068	0.0	0.0	0.7951
-LEU	137	A	0.5	0.6911	0.7058	0.7842	1.0	0.7842	0.0	0.0	0.745
-THR	138	A	1.0	0.505	0.3257	0.4486	0.88	0.3948	0.0	0.0	0.4499
-THR	139	A	1.0	0.5607	0.3257	0.5776	0.92	0.5313	0.0	0.0	0.546
-ILE	140	A	1.0	0.593	0.638	0.58	0.98	0.5684	0.0	0.0	0.6155
-GLY	141	A	1.0	0.4358	0.4117	0.9101	1.0	0.9101	0.0	0.0	0.673
-GLY	142	A	0.8	0.5189	0.4117	0.92	1.0	0.92	0.0	0.0	0.7194
-PRO	143	A	1.0	0.5518	0.466	0.8312	1.0	0.8312	0.0	0.0	0.6915
-LYS	144	A	1.0	0.354	0.2488	0.4453	0.94	0.4186	0.0	0.0	0.3863
-GLU	145	A	1.0	0.4377	0.3348	0.5495	1.0	0.5495	0.0	0.0	0.4936
-LEU	146	A	0.8	0.6906	0.7058	0.6933	1.0	0.6933	0.0	0.0	0.6996
-THR	147	A	1.0	0.52	0.3257	0.788	1.0	0.788	0.0	0.0	0.654
-ALA	148	A	1.0	0.4216	0.3846	0.5145	1.0	0.5145	0.0	0.0	0.468
-PHE	149	A	1.0	0.5765	1.0	0.7179	1.0	0.7179	0.0	0.0	0.859
-LEU	150	A	0.5	0.636	0.7058	0.6156	1.0	0.6156	0.0	0.0	0.6709
-HIS	151	A	1.0	0.3909	0.5972	0.7796	1.0	0.7796	0.0	0.0	0.6884
-ASN	152	A	1.0	0.3704	0.3936	0.4439	0.96	0.4262	0.0	0.0	0.4099
-MET	153	A	1.0	0.522	0.6606	0.562	0.96	0.5395	0.0	0.0	0.6
-GLY	154	A	1.0	0.4098	0.4117	0.901	1.0	0.901	0.0	0.0	0.6564
-ASP	155	A	0.8	0.5428	0.3212	0.8998	1.0	0.8998	0.0	0.0	0.7213
-HIS	156	A	1.0	0.3581	0.5972	0.3194	0.98	0.3131	0.0	0.0	0.4776
-VAL	157	A	1.0	0.4988	0.5656	0.4669	0.98	0.4576	0.0	0.0	0.5322
-THR	158	A	0.8	0.6713	0.3257	0.7055	1.0	0.7055	0.0	0.0	0.7055
-ARG	159	A	1.0	0.5047	0.5067	0.8208	1.0	0.8208	0.0	0.0	0.8208
-LEU	160	A	0.8	0.6849	0.7058	0.7638	1.0	0.7638	0.0	0.0	0.7638
-ASP	161	A	1.0	0.5004	0.3212	0.8324	1.0	0.8324	0.0	0.0	0.8324
-ARG	162	A	1.0	0.4994	0.5067	0.8001	1.0	0.8001	0.0	0.0	0.8001
-TRP	163	A	1.0	0.5305	0.9909	0.4471	0.96	0.4292	0.6565	1.0	0.4292
-GLU	164	A	0.8	0.675	0.3348	0.8706	1.0	0.8706	0.0	0.0	0.7728
-PRO	165	A	1.0	0.5174	0.466	0.681	1.0	0.681	0.0	0.0	0.5992
-GLU	166	A	1.0	0.4656	0.3348	0.472	0.9	0.4248	0.0	0.0	0.4452
-LEU	167	A	0.8	0.6894	0.7058	0.8229	1.0	0.8229	0.0	0.0	0.7644
-ASN	168	A	1.0	0.6465	0.3936	0.8211	1.0	0.8211	0.5738	1.0	0.7338
-GLU	169	A	1.0	0.4575	0.3348	0.5883	1.0	0.5883	0.0	0.0	0.5229
-ALA	170	A	1.0	0.5691	0.3846	0.674	1.0	0.674	0.0	0.0	0.6216
-ILE	171	A	1.0	0.3772	0.638	0.3896	0.98	0.3818	0.0	0.0	0.5099
-PRO	172	A	1.0	0.3669	0.466	0.7768	1.0	0.7768	0.0	0.0	0.6214
-ASN	173	A	1.0	0.336	0.3936	0.6994	1.0	0.6994	0.0	0.0	0.5465
-ASP	174	A	1.0	0.4217	0.3212	0.8039	1.0	0.8039	0.0	0.0	0.6128
-GLU	175	A	1.0	0.4207	0.3348	0.579	0.96	0.5559	0.0	0.0	0.4883
-ARG	176	A	1.0	0.423	0.5067	0.7876	1.0	0.7876	0.0	0.0	0.6472
-ASP	177	A	0.8	0.6535	0.3212	0.918	1.0	0.918	0.0	0.0	0.7857
-THR	178	A	1.0	0.6457	0.3257	0.8561	1.0	0.8561	0.0	0.0	0.7509
-THR	179	A	0.5	0.7536	0.3257	0.8062	1.0	0.8062	0.0	0.0	0.7799
-MET	180	A	1.0	0.5708	0.6606	0.7298	1.0	0.7298	0.0	0.0	0.6952
-PRO	181	A	0.5	0.723	0.466	0.8848	1.0	0.8848	0.0	0.0	0.8039
-ALA	182	A	1.0	0.598	0.3846	0.4338	0.96	0.4164	0.0	0.0	0.5072
-ALA	183	A	1.0	0.6268	0.3846	0.809	1.0	0.809	0.0	0.0	0.7179
-MET	184	A	0.5	0.8376	0.6606	0.7792	1.0	0.7792	0.0	0.0	0.8084
-ALA	185	A	0.5	0.7466	0.3846	0.5576	1.0	0.5576	0.0	0.0	0.6521
-THR	186	A	1.0	0.584	0.3257	0.4016	0.84	0.3373	0.0	0.0	0.4606
-THR	187	A	0.8	0.7083	0.3257	0.735	1.0	0.735	0.0	0.0	0.7216
-LEU	188	A	0.5	0.846	0.7058	0.8024	1.0	0.8024	0.0	0.0	0.8242
-ARG	189	A	1.0	0.5527	0.5067	0.4245	0.96	0.4075	0.0	0.0	0.5297
-LYS	190	A	1.0	0.5328	0.2488	0.392	1.0	0.392	0.0	0.0	0.4624
-LEU	191	A	0.5	0.7328	0.7058	0.7264	1.0	0.7264	0.0	0.0	0.7296
-LEU	192	A	0.8	0.7139	0.7058	0.629	1.0	0.629	0.0	0.0	0.7098
-THR	193	A	1.0	0.5278	0.3257	0.5915	1.0	0.5915	0.0	0.0	0.5596
-GLY	194	A	1.0	0.478	0.4117	0.8133	1.0	0.8133	0.0	0.0	0.6457
-GLU	195	A	1.0	0.3446	0.3348	0.4892	0.9	0.4403	0.0	0.0	0.3924
-LEU	196	A	1.0	0.5054	0.7058	0.4992	0.92	0.4593	0.0	0.0	0.6056
-LEU	197	A	0.8	0.5703	0.7058	0.9434	1.0	0.9434	0.0	0.0	0.8246
-THR	198	A	1.0	0.3877	0.3257	0.5824	1.0	0.5824	0.0	0.0	0.485
-LEU	199	A	1.0	0.3445	0.7058	0.3969	0.8	0.3175	0.0	0.0	0.5252
-ALA	200	A	1.0	0.386	0.3846	0.4251	0.98	0.4166	0.0	0.0	0.4013
-SER	201	A	0.8	0.5245	0.3574	0.8076	1.0	0.8076	0.0	0.0	0.666
-ARG	202	A	1.0	0.4966	0.5067	0.7406	1.0	0.7406	0.0	0.0	0.6236
-GLN	203	A	1.0	0.4657	0.4343	0.3721	0.8	0.2977	0.0	0.0	0.45
-GLN	204	A	1.0	0.5485	0.4343	0.5601	1.0	0.5601	0.0	0.0	0.5543
-LEU	205	A	0.5	0.7577	0.7058	0.8828	1.0	0.8828	0.0	0.0	0.8202
-ILE	206	A	1.0	0.6366	0.638	0.4625	0.92	0.4255	0.0	0.0	0.6373
-ASP	207	A	1.0	0.5326	0.3212	0.4118	0.94	0.3871	0.0	0.0	0.4598
-TRP	208	A	0.8	0.6672	0.9909	0.8299	1.0	0.8299	0.0	0.0	0.9104
-MET	209	A	0.5	0.7957	0.6606	0.7864	1.0	0.7864	0.0	0.0	0.791
-GLU	210	A	1.0	0.5437	0.3348	0.3948	1.0	0.3948	0.0	0.0	0.4692
-ALA	211	A	1.0	0.5428	0.3846	0.5405	0.96	0.5189	0.0	0.0	0.5308
-ASP	212	A	1.0	0.6481	0.3212	0.6863	1.0	0.6863	0.0	0.0	0.6672
-LYS	213	A	1.0	0.474	0.2488	0.4409	0.96	0.4233	0.0	0.0	0.4486
-VAL	214	A	1.0	0.6057	0.5656	0.8586	1.0	0.8586	0.6338	1.0	0.7322
-ALA	215	A	0.5	0.6521	0.3846	0.848	1.0	0.848	0.0	0.0	0.75
-GLY	216	A	1.0	0.5019	0.4117	0.556	1.0	0.556	0.0	0.0	0.529
-PRO	217	A	1.0	0.4821	0.466	0.4396	1.0	0.4396	0.0	0.0	0.474
-LEU	218	A	0.5	0.6631	0.7058	0.7855	1.0	0.7855	0.0	0.0	0.7456
-LEU	219	A	0.8	0.7409	0.7058	0.7473	1.0	0.7473	0.0	0.0	0.7441
-ARG	220	A	1.0	0.5678	0.5067	0.8248	1.0	0.8248	0.0	0.0	0.6963
-SER	221	A	1.0	0.4591	0.3574	0.7973	1.0	0.7973	0.0	0.0	0.6282
-ALA	222	A	1.0	0.4909	0.3846	0.7543	1.0	0.7543	0.0	0.0	0.6226
-LEU	223	A	1.0	0.5015	0.7058	0.7806	0.98	0.765	0.0	0.0	0.7354
-PRO	224	A	1.0	0.3538	0.466	0.8972	1.0	0.8972	0.0	0.0	0.6816
-ALA	225	A	1.0	0.2464	0.3846	0.3912	0.88	0.3442	0.0	0.0	0.3644
-GLY	226	A	1.0	0.2821	0.4117	0.5641	1.0	0.5641	0.0	0.0	0.4879
-TRP	227	A	1.0	0.4327	0.9909	0.8583	1.0	0.8583	0.0	0.0	0.9246
-PHE	228	A	1.0	0.5177	1.0	0.4604	0.96	0.442	0.0	0.0	0.7588
-ILE	229	A	1.0	0.628	0.638	0.7273	1.0	0.7273	0.0	0.0	0.6826
-ALA	230	A	0.5	0.7157	0.3846	0.7834	1.0	0.7834	0.0	0.0	0.7495
-ASP	231	A	0.5	0.78	0.3212	0.8777	1.0	0.8777	0.0	0.0	0.8288
-LYS	232	A	0.5	0.8575	0.2488	0.8946	1.0	0.8946	0.0	0.0	0.876
-SER	233	A	0.8	0.793	0.3574	0.8829	1.0	0.8829	0.0	0.0	0.838
-GLY	234	A	0.8	0.8195	0.4117	0.9476	1.0	0.9476	0.0	0.0	0.8836
-ALA	235	A	1.0	0.6882	0.3846	0.6626	1.0	0.6626	0.0	0.0	0.6754
-GLY	236	A	1.0	0.6274	0.4117	0.7509	1.0	0.7509	0.5643	1.0	0.6891
-GLU	237	A	1.0	0.482	0.3348	0.4952	0.94	0.4654	0.0	0.0	0.4737
-ARG	238	A	1.0	0.4196	0.5067	0.585	1.0	0.585	0.0	0.0	0.5458
-GLY	239	A	1.0	0.5384	0.4117	0.7475	1.0	0.7475	0.0	0.0	0.643
-SER	240	A	0.8	0.6602	0.3574	0.6542	1.0	0.6542	0.0	0.0	0.6572
-ARG	241	A	1.0	0.7045	0.5067	0.5641	1.0	0.5641	0.0	0.0	0.6343
-GLY	242	A	0.5	0.8695	0.4117	0.8193	1.0	0.8193	0.0	0.0	0.8444
-ILE	243	A	0.5	0.8867	0.638	0.8821	1.0	0.8821	0.0	0.0	0.8844
-ILE	244	A	0.5	1.0	0.638	0.6077	1.0	0.6077	0.0	0.0	0.819
-ALA	245	A	0.5	0.8736	0.3846	0.832	1.0	0.832	0.0	0.0	0.8528
-ALA	246	A	0.5	0.7637	0.3846	0.5933	1.0	0.5933	0.0	0.0	0.6785
-LEU	247	A	0.8	0.6955	0.7058	0.522	0.98	0.5116	0.0	0.0	0.7006
-GLY	248	A	0.5	0.5269	0.4117	0.7481	1.0	0.7481	0.0	0.0	0.6375
-PRO	249	A	1.0	0.3818	0.466	0.8488	1.0	0.8488	0.0	0.0	0.6574
-ASP	250	A	1.0	0.2685	0.3212	0.7141	0.98	0.6998	0.0	0.0	0.5105
-GLY	251	A	1.0	0.3519	0.4117	0.7147	0.96	0.6861	0.0	0.0	0.5489
-LYS	252	A	1.0	0.3777	0.2488	0.557	0.96	0.5347	0.0	0.0	0.4562
-PRO	253	A	1.0	0.5517	0.466	0.4431	0.94	0.4165	0.0	0.0	0.5088
-SER	254	A	1.0	0.5022	0.3574	0.7783	1.0	0.7783	0.0	0.0	0.6402
-ARG	255	A	1.0	0.5697	0.5067	0.5295	1.0	0.5295	0.0	0.0	0.5496
-ILE	256	A	0.5	0.7646	0.638	0.6104	1.0	0.6104	0.0	0.0	0.7013
-VAL	257	A	0.5	0.8492	0.5656	0.5592	1.0	0.5592	0.0	0.0	0.7074
-VAL	258	A	0.5	0.9025	0.5656	0.5984	1.0	0.5984	0.0	0.0	0.7505
-ILE	259	A	0.5	0.8927	0.638	0.6416	1.0	0.6416	0.0	0.0	0.7672
-TYR	260	A	0.8	0.8772	0.7963	0.7728	1.0	0.7728	0.0	0.0	0.8368
-THR	261	A	0.8	0.7217	0.3257	0.6266	1.0	0.6266	0.0	0.0	0.6742
-THR	262	A	1.0	0.6203	0.3257	0.595	1.0	0.595	0.0	0.0	0.6076
-GLY	263	A	1.0	0.4815	0.4117	0.5253	0.94	0.4938	0.0	0.0	0.4876
-SER	264	A	0.8	0.4788	0.3574	0.5525	0.98	0.5414	0.0	0.0	0.5101
-GLN	265	A	1.0	0.3055	0.4343	0.3663	0.58	0.2124	0.0	0.0	0.3699
-ALA	266	A	1.0	0.3944	0.3846	0.5192	1.0	0.5192	0.0	0.0	0.4568
-THR	267	A	1.0	0.322	0.3257	0.4979	0.9	0.4481	0.0	0.0	0.3869
-MET	268	A	1.0	0.4751	0.6606	0.5062	1.0	0.5062	0.5384	1.0	0.5834
-ASP	269	A	1.0	0.3583	0.3212	0.401	0.96	0.3849	0.0	0.0	0.3716
-GLU	270	A	1.0	0.3681	0.3348	0.4038	0.96	0.3876	0.0	0.0	0.3778
-ARG	271	A	1.0	0.5589	0.5067	0.6372	1.0	0.6372	0.0	0.0	0.598
-ASN	272	A	1.0	0.5374	0.3936	0.5862	1.0	0.5862	0.0	0.0	0.5618
-ARG	273	A	1.0	0.3798	0.5067	0.5628	0.98	0.5516	0.0	0.0	0.5292
-GLN	274	A	1.0	0.5361	0.4343	0.5753	0.98	0.5638	0.0	0.0	0.5499
-ILE	275	A	0.5	0.7372	0.638	0.6805	1.0	0.6805	0.0	0.0	0.7088
-ALA	276	A	1.0	0.5733	0.3846	0.7999	1.0	0.7999	0.0	0.0	0.6866
-GLU	277	A	1.0	0.4906	0.3348	0.4883	0.84	0.4102	0.0	0.0	0.4504
-ILE	278	A	0.8	0.7031	0.638	0.6801	1.0	0.6801	0.0	0.0	0.6916
-GLY	279	A	0.5	0.6544	0.4117	0.6752	1.0	0.6752	0.0	0.0	0.6648
-ALA	280	A	1.0	0.4945	0.3846	0.6462	1.0	0.6462	0.0	0.0	0.5704
-SER	281	A	1.0	0.5238	0.3574	0.5353	0.9	0.4817	0.0	0.0	0.5028
-LEU	282	A	0.8	0.6582	0.7058	0.5349	0.98	0.5242	0.0	0.0	0.682
-ILE	283	A	1.0	0.508	0.638	0.4816	0.98	0.472	0.0	0.0	0.573
-LYS	284	A	1.0	0.3538	0.2488	0.3331	0.68	0.2265	0.0	0.0	0.3013
-HIS	285	A	1.0	0.4294	0.5972	0.1371	0.46	0.063	0.0	0.0	0.5133
-TRP	286	A	1.0	0.4871	0.9909	0.2251	0.74	0.1666	0.0	0.0	0.739
+AA  pos chain pc     tr     freq trace  
+MET 1   A     0.6606 0.0    0.0  0.0    
+SER 2   A     0.3574 0.0    0.0  0.0    
+ILE 3   A     0.638  0.0    0.0  0.0    
+GLN 4   A     0.4343 0.1189 0.22 0.0261 
+HIS 5   A     0.5972 0.0763 0.18 0.0137 
+PHE 6   A     1.0    0.0465 0.04 0.0018 
+ARG 7   A     0.5067 0.0853 0.4  0.0341 
+VAL 8   A     0.5656 0.088  0.6  0.0528 
+ALA 9   A     0.3846 0.1063 0.56 0.0595 
+LEU 10  A     0.7058 0.0746 0.14 0.0104 
+ILE 11  A     0.638  0.0817 0.4  0.0327 
+PRO 12  A     0.466  0.09   0.4  0.036  
+PHE 13  A     1.0    0.1315 0.82 0.1078 
+PHE 14  A     1.0    0.0858 0.26 0.0223 
+ALA 15  A     0.3846 0.1997 0.84 0.1678 
+ALA 16  A     0.3846 0.2801 0.36 0.1008 
+PHE 17  A     1.0    0.1378 0.78 0.1074 
+CYS 18  A     0.6425 0.1642 0.6  0.0985 
+LEU 19  A     0.7058 0.2308 0.9  0.2077 
+PRO 20  A     0.466  0.2446 0.88 0.2152 
+VAL 21  A     0.5656 0.2416 0.62 0.1498 
+PHE 22  A     1.0    0.2421 0.46 0.1113 
+ALA 23  A     0.3846 0.3107 0.92 0.2858 
+HIS 24  A     0.5972 0.2717 0.66 0.1793 
+PRO 25  A     0.466  0.2763 0.86 0.2376 
+GLU 26  A     0.3348 0.298  0.82 0.2443 
+THR 27  A     0.3257 0.5272 0.98 0.5166 
+LEU 28  A     0.7058 0.3125 0.96 0.3    
+VAL 29  A     0.5656 0.2721 0.78 0.2122 
+LYS 30  A     0.2488 0.3511 0.88 0.309  
+VAL 31  A     0.5656 0.5904 1.0  0.5904 
+LYS 32  A     0.2488 0.4791 0.86 0.412  
+ASP 33  A     0.3212 0.4265 0.58 0.2473 
+ALA 34  A     0.3846 0.6508 1.0  0.6508 
+GLU 35  A     0.3348 0.826  1.0  0.826  
+ASP 36  A     0.3212 0.332  0.78 0.259  
+GLN 37  A     0.4343 0.4018 0.94 0.3777 
+LEU 38  A     0.7058 0.5015 1.0  0.5015 
+GLY 39  A     0.4117 0.6516 0.94 0.6125 
+ALA 40  A     0.3846 0.7891 1.0  0.7891 
+ARG 41  A     0.5067 0.7611 1.0  0.7611 
+VAL 42  A     0.5656 0.6983 1.0  0.6983 
+GLY 43  A     0.4117 0.9231 1.0  0.9231 
+TYR 44  A     0.7963 0.7409 1.0  0.7409 
+ILE 45  A     0.638  0.5836 0.98 0.5719 
+GLU 46  A     0.3348 0.6177 1.0  0.6177 
+LEU 47  A     0.7058 0.5381 1.0  0.5381 
+ASP 48  A     0.3212 0.7325 1.0  0.7325 
+LEU 49  A     0.7058 0.6244 1.0  0.6244 
+ASN 50  A     0.3936 0.4483 0.92 0.4124 
+SER 51  A     0.3574 0.4474 0.98 0.4385 
+GLY 52  A     0.4117 0.7082 1.0  0.7082 
+LYS 53  A     0.2488 0.3277 0.9  0.2949 
+ILE 54  A     0.638  0.4006 0.92 0.3686 
+LEU 55  A     0.7058 0.4637 0.98 0.4545 
+GLU 56  A     0.3348 0.3943 0.58 0.2287 
+SER 57  A     0.3574 0.3803 0.8  0.3042 
+PHE 58  A     1.0    0.4781 1.0  0.4781 
+ARG 59  A     0.5067 0.7779 1.0  0.7779 
+PRO 60  A     0.466  0.6132 0.98 0.6009 
+GLU 61  A     0.3348 0.5916 0.94 0.5561 
+GLU 62  A     0.3348 0.7667 1.0  0.7667 
+ARG 63  A     0.5067 0.7829 1.0  0.7829 
+PHE 64  A     1.0    0.8674 1.0  0.8674 
+PRO 65  A     0.466  0.7794 1.0  0.7794 
+MET 66  A     0.6606 0.683  1.0  0.683  
+MET 67  A     0.6606 0.7854 1.0  0.7854 
+SER 68  A     0.3574 0.9524 1.0  0.9524 
+THR 69  A     0.3257 0.862  1.0  0.862  
+PHE 70  A     1.0    0.7709 1.0  0.7709 
+LYS 71  A     0.2488 0.9509 1.0  0.9509 
+VAL 72  A     0.5656 0.6133 1.0  0.6133 
+LEU 73  A     0.7058 0.7036 0.98 0.6895 
+LEU 74  A     0.7058 0.7025 1.0  0.7025 
+CYS 75  A     0.6425 0.8082 1.0  0.8082 
+GLY 76  A     0.4117 0.6512 1.0  0.6512 
+ALA 77  A     0.3846 0.6874 1.0  0.6874 
+VAL 78  A     0.5656 0.5935 1.0  0.5935 
+LEU 79  A     0.7058 0.9274 1.0  0.9274 
+SER 80  A     0.3574 0.5041 0.98 0.494  
+ARG 81  A     0.5067 0.6744 1.0  0.6744 
+VAL 82  A     0.5656 0.6939 1.0  0.6939 
+ASP 83  A     0.3212 0.8106 1.0  0.8106 
+ALA 84  A     0.3846 0.42   0.96 0.4032 
+GLY 85  A     0.4117 0.8478 1.0  0.8478 
+GLN 86  A     0.4343 0.4545 0.94 0.4272 
+GLU 87  A     0.3348 0.6987 1.0  0.6987 
+GLN 88  A     0.4343 0.4268 0.96 0.4097 
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+PRO 172 A     0.466  0.775  1.0  0.775  
+ASN 173 A     0.3936 0.7097 1.0  0.7097 
+ASP 174 A     0.3212 0.8141 1.0  0.8141 
+GLU 175 A     0.3348 0.6269 0.96 0.6018 
+ARG 176 A     0.5067 0.793  1.0  0.793  
+ASP 177 A     0.3212 0.9192 1.0  0.9192 
+THR 178 A     0.3257 0.8578 1.0  0.8578 
+THR 179 A     0.3257 0.8116 1.0  0.8116 
+MET 180 A     0.6606 0.7428 1.0  0.7428 
+PRO 181 A     0.466  0.8968 1.0  0.8968 
+ALA 182 A     0.3846 0.3608 0.92 0.3319 
+ALA 183 A     0.3846 0.8123 1.0  0.8123 
+MET 184 A     0.6606 0.7583 1.0  0.7583 
+ALA 185 A     0.3846 0.5829 1.0  0.5829 
+THR 186 A     0.3257 0.3149 0.72 0.2267 
+THR 187 A     0.3257 0.6736 1.0  0.6736 
+LEU 188 A     0.7058 0.8609 1.0  0.8609 
+ARG 189 A     0.5067 0.4587 1.0  0.4587 
+LYS 190 A     0.2488 0.4026 0.98 0.3945 
+LEU 191 A     0.7058 0.7247 1.0  0.7247 
+LEU 192 A     0.7058 0.6253 1.0  0.6253 
+THR 193 A     0.3257 0.624  0.98 0.6115 
+GLY 194 A     0.4117 0.7908 1.0  0.7908 
+GLU 195 A     0.3348 0.4492 0.86 0.3863 
+LEU 196 A     0.7058 0.5504 0.96 0.5284 
+LEU 197 A     0.7058 0.9508 1.0  0.9508 
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+SER 201 A     0.3574 0.8099 1.0  0.8099 
+ARG 202 A     0.5067 0.7575 1.0  0.7575 
+GLN 203 A     0.4343 0.3579 0.8  0.2863 
+GLN 204 A     0.4343 0.58   1.0  0.58   
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+ILE 206 A     0.638  0.3835 0.96 0.3681 
+ASP 207 A     0.3212 0.3549 0.92 0.3265 
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+VAL 214 A     0.5656 0.8561 1.0  0.8561 
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+GLY 226 A     0.4117 0.605  1.0  0.605  
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+ALA 230 A     0.3846 0.779  1.0  0.779  
+ASP 231 A     0.3212 0.8807 1.0  0.8807 
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+GLY 236 A     0.4117 0.7357 0.98 0.7209 
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+ARG 238 A     0.5067 0.5564 1.0  0.5564 
+GLY 239 A     0.4117 0.7577 1.0  0.7577 
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+ARG 241 A     0.5067 0.6065 1.0  0.6065 
+GLY 242 A     0.4117 0.8227 1.0  0.8227 
+ILE 243 A     0.638  0.8901 1.0  0.8901 
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+ALA 245 A     0.3846 0.8326 1.0  0.8326 
+ALA 246 A     0.3846 0.5205 1.0  0.5205 
+LEU 247 A     0.7058 0.5266 1.0  0.5266 
+GLY 248 A     0.4117 0.7221 1.0  0.7221 
+PRO 249 A     0.466  0.846  1.0  0.846  
+ASP 250 A     0.3212 0.6597 1.0  0.6597 
+GLY 251 A     0.4117 0.7006 0.98 0.6866 
+LYS 252 A     0.2488 0.5441 0.98 0.5332 
+PRO 253 A     0.466  0.5196 0.82 0.4261 
+SER 254 A     0.3574 0.7731 1.0  0.7731 
+ARG 255 A     0.5067 0.5066 1.0  0.5066 
+ILE 256 A     0.638  0.6053 0.98 0.5932 
+VAL 257 A     0.5656 0.5454 1.0  0.5454 
+VAL 258 A     0.5656 0.5792 0.96 0.556  
+ILE 259 A     0.638  0.6305 1.0  0.6305 
+TYR 260 A     0.7963 0.7411 1.0  0.7411 
+THR 261 A     0.3257 0.6469 1.0  0.6469 
+THR 262 A     0.3257 0.6117 1.0  0.6117 
+GLY 263 A     0.4117 0.5274 0.96 0.5063 
+SER 264 A     0.3574 0.5703 0.98 0.5589 
+GLN 265 A     0.4343 0.3536 0.64 0.2263 
+ALA 266 A     0.3846 0.5041 1.0  0.5041 
+THR 267 A     0.3257 0.5037 0.92 0.4634 
+MET 268 A     0.6606 0.4767 1.0  0.4767 
+ASP 269 A     0.3212 0.4463 0.86 0.3838 
+GLU 270 A     0.3348 0.3459 1.0  0.3459 
+ARG 271 A     0.5067 0.6866 1.0  0.6866 
+ASN 272 A     0.3936 0.5813 1.0  0.5813 
+ARG 273 A     0.5067 0.541  1.0  0.541  
+GLN 274 A     0.4343 0.5579 0.98 0.5467 
+ILE 275 A     0.638  0.6625 1.0  0.6625 
+ALA 276 A     0.3846 0.7927 1.0  0.7927 
+GLU 277 A     0.3348 0.5175 0.72 0.3726 
+ILE 278 A     0.638  0.6661 1.0  0.6661 
+GLY 279 A     0.4117 0.6646 1.0  0.6646 
+ALA 280 A     0.3846 0.6007 0.96 0.5767 
+SER 281 A     0.3574 0.5172 0.96 0.4965 
+LEU 282 A     0.7058 0.5673 0.96 0.5446 
+ILE 283 A     0.638  0.5761 0.98 0.5646 
+LYS 284 A     0.2488 0.3268 0.48 0.1569 
+HIS 285 A     0.5972 0.166  0.44 0.073  
+TRP 286 A     0.9909 0.2312 0.66 0.1526 

docs/_build/html/_sources/analysis.rst.txt

-Analyzing and Modifying the PRESCOTT Output
+Analyzing and Modifying the ESCOTT Output
 ==========================================
 
-Raw PRESCOTT Scores and Their Interpretation
+Raw ESCOTT Scores and Their Interpretation
 -------------------------------------------
-There is not a hardcoded limit for raw PRESCOTT scores. However, the values
+There is not a hardcoded limit for raw ESCOTT scores. However, the values
 range between [-12, 2] generally. The lower values mean the mutations is impactful, 
 while values close to 0 means the mutation does not have any significant impact.
 
@@ -13,7 +13,7 @@ it is not always the case.
 Entire Single Point Mutation Landscape Calculations
 ---------------------------------------------------
 
-By default, PRESCOTT will only output the combined (independent
+By default, ESCOTT will only output the combined (independent
 and epistatic) scores*: 
 
 There are three output files:

docs/_build/html/_sources/index.rst.txt

-.. esgemme documentation master file, created by
+.. PRESCOTT documentation master file, created by
    sphinx-quickstart on Fri May  5 13:52:13 2023.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to esgemme's documentation!
+Welcome to PRESCOTT documentation!
 ===================================
 
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
 
+   introduction.rst
    docker.rst
    analysis.rst
    input-preparation.rst

docs/_build/html/analysis.html

@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Analyzing and Modifying the PRESCOTT Output &mdash; prescott 1.5.0 documentation</title>
+  <title>Analyzing and Modifying the ESCOTT Output &mdash; prescott 1.5.0 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -20,7 +20,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Preparing Your Own Input" href="input-preparation.html" />
-    <link rel="prev" title="Using PRESCOTT via Docker" href="docker.html" /> 
+    <link rel="prev" title="Using ESCOTT via Docker" href="docker.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -44,9 +44,12 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="docker.html">Using PRESCOTT via Docker</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="#">Analyzing and Modifying the PRESCOTT Output</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#raw-prescott-scores-and-their-interpretation">Raw PRESCOTT Scores and Their Interpretation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="introduction.html"></a></li>
+<li class="toctree-l1"><a class="reference internal" href="introduction.html#prescott-population-aware-epistatic-and-structural-model-of-mutational-effects">PRESCOTT: Population awaRe Epistatic and StruCtural mOdel of muTational effecTs</a></li>
+<li class="toctree-l1"><a class="reference internal" href="introduction.html#cite">Cite</a></li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Analyzing and Modifying the ESCOTT Output</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#raw-escott-scores-and-their-interpretation">Raw ESCOTT Scores and Their Interpretation</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#entire-single-point-mutation-landscape-calculations">Entire Single Point Mutation Landscape Calculations</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#selected-single-point-or-multiple-point-mutation-calculations">Selected Single Point or Multiple Point Mutation Calculations</a></li>
 </ul>
@@ -69,7 +72,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
-      <li class="breadcrumb-item active">Analyzing and Modifying the PRESCOTT Output</li>
+      <li class="breadcrumb-item active">Analyzing and Modifying the ESCOTT Output</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/analysis.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -79,11 +82,11 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
              
-  <section id="analyzing-and-modifying-the-prescott-output">
-<h1>Analyzing and Modifying the PRESCOTT Output<a class="headerlink" href="#analyzing-and-modifying-the-prescott-output" title="Permalink to this heading"></a></h1>
-<section id="raw-prescott-scores-and-their-interpretation">
-<h2>Raw PRESCOTT Scores and Their Interpretation<a class="headerlink" href="#raw-prescott-scores-and-their-interpretation" title="Permalink to this heading"></a></h2>
-<p>There is not a hardcoded limit for raw PRESCOTT scores. However, the values
+  <section id="analyzing-and-modifying-the-escott-output">
+<h1>Analyzing and Modifying the ESCOTT Output<a class="headerlink" href="#analyzing-and-modifying-the-escott-output" title="Permalink to this heading"></a></h1>
+<section id="raw-escott-scores-and-their-interpretation">
+<h2>Raw ESCOTT Scores and Their Interpretation<a class="headerlink" href="#raw-escott-scores-and-their-interpretation" title="Permalink to this heading"></a></h2>
+<p>There is not a hardcoded limit for raw ESCOTT scores. However, the values
 range between [-12, 2] generally. The lower values mean the mutations is impactful,
 while values close to 0 means the mutation does not have any significant impact.</p>
 <p>We should note that most of the ‘impactful’ mutations are deleterious but
@@ -91,7 +94,7 @@ it is not always the case.</p>
 </section>
 <section id="entire-single-point-mutation-landscape-calculations">
 <h2>Entire Single Point Mutation Landscape Calculations<a class="headerlink" href="#entire-single-point-mutation-landscape-calculations" title="Permalink to this heading"></a></h2>
-<p>By default, PRESCOTT will only output the combined (independent
+<p>By default, ESCOTT will only output the combined (independent
 and epistatic) scores*:</p>
 <p>There are three output files:</p>
 <ol class="arabic">
@@ -143,7 +146,7 @@ D286F -0.23</p>
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="docker.html" class="btn btn-neutral float-left" title="Using PRESCOTT via Docker" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="docker.html" class="btn btn-neutral float-left" title="Using ESCOTT via Docker" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="input-preparation.html" class="btn btn-neutral float-right" title="Preparing Your Own Input" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 

docs/_build/html/genindex.html

@@ -41,8 +41,9 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
-<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the PRESCOTT Output</a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESCOTT Output</a></li>
 <li class="toctree-l1"><a class="reference internal" href="input-preparation.html">Preparing Your Own Input</a></li>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 </ul>

docs/_build/html/index.html

@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Welcome to esgemme’s documentation! &mdash; prescott 1.5.0 documentation</title>
+  <title>Welcome to PRESCOTT documentation! &mdash; prescott 1.5.0 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -19,7 +19,7 @@
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="Using ESCOTT via Docker" href="docker.html" /> 
+    <link rel="next" title="Introduction" href="introduction.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -43,8 +43,9 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
-<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the PRESCOTT Output</a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESCOTT Output</a></li>
 <li class="toctree-l1"><a class="reference internal" href="input-preparation.html">Preparing Your Own Input</a></li>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 </ul>
@@ -63,7 +64,7 @@
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@@ -73,11 +74,19 @@
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-  <section id="welcome-to-esgemme-s-documentation">
-<h1>Welcome to esgemme’s documentation!<a class="headerlink" href="#welcome-to-esgemme-s-documentation" title="Permalink to this heading"></a></h1>
+  <section id="welcome-to-prescott-documentation">
+<h1>Welcome to PRESCOTT documentation!<a class="headerlink" href="#welcome-to-prescott-documentation" title="Permalink to this heading"></a></h1>
 <div class="toctree-wrapper compound">
 <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="introduction.html#what-is-prescott">What is PRESCOTT?</a></li>
+<li class="toctree-l2"><a class="reference internal" href="introduction.html#input-data-requirements">Input Data Requirements</a></li>
+<li class="toctree-l2"><a class="reference internal" href="introduction.html#usage">Usage</a></li>
+<li class="toctree-l2"><a class="reference internal" href="introduction.html#installation">Installation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="introduction.html#citation">Citation</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="docker.html#requirements">Requirements</a></li>
 <li class="toctree-l2"><a class="reference internal" href="docker.html#getting-the-example-input-data">Getting the example input data</a></li>
@@ -86,8 +95,8 @@
 <li class="toctree-l2"><a class="reference internal" href="docker.html#running-several-jobs-using-docker">Running several jobs using docker</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the PRESCOTT Output</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="analysis.html#raw-prescott-scores-and-their-interpretation">Raw PRESCOTT Scores and Their Interpretation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESCOTT Output</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="analysis.html#raw-escott-scores-and-their-interpretation">Raw ESCOTT Scores and Their Interpretation</a></li>
 <li class="toctree-l2"><a class="reference internal" href="analysis.html#entire-single-point-mutation-landscape-calculations">Entire Single Point Mutation Landscape Calculations</a></li>
 <li class="toctree-l2"><a class="reference internal" href="analysis.html#selected-single-point-or-multiple-point-mutation-calculations">Selected Single Point or Multiple Point Mutation Calculations</a></li>
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@@ -118,7 +127,7 @@
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+<li class="toctree-l1 current"><a class="current reference internal" href="#">Introduction</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#what-is-prescott">What is PRESCOTT?</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#input-data-requirements">Input Data Requirements</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#input-data-requirements-for-escott">Input Data Requirements for escott</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#input-data-requirements-for-prescott">Input Data Requirements for prescott</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#usage">Usage</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#running-the-escott-program">Running the escott program</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#running-the-prescott-program">Running the prescott program</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#installation">Installation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#citation">Citation</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESCOTT Output</a></li>
+<li class="toctree-l1"><a class="reference internal" href="input-preparation.html">Preparing Your Own Input</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
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+           <div itemprop="articleBody">
+             
+  <section id="introduction">
+<h1>Introduction<a class="headerlink" href="#introduction" title="Permalink to this heading"></a></h1>
+<section id="what-is-prescott">
+<h2>What is PRESCOTT?<a class="headerlink" href="#what-is-prescott" title="Permalink to this heading"></a></h2>
+<p>PRESCOTT (PRESCOTT: Population awaRe Epistatic and StruCtural mOdel of muTational effecTs) is a package predicting mutational effects in a protein based
+on population, evolutionary and structural information. It is made up of
+two main programs: escott and prescott.</p>
+<p>ESCOTT can calculate effects of single point mutations and multiple
+point mutations. On the other hand, PRESCOTT incorporates population
+frequencies into ESCOTT predictions. Therefore, you need to run ESCOTT
+first to have predictions of mutational effects. We recommend using
+PRESCOTT package via our web site or our docker image due to its
+dependencies.</p>
+</section>
+<section id="input-data-requirements">
+<h2>Input Data Requirements<a class="headerlink" href="#input-data-requirements" title="Permalink to this heading"></a></h2>
+<section id="input-data-requirements-for-escott">
+<h3>Input Data Requirements for escott<a class="headerlink" href="#input-data-requirements-for-escott" title="Permalink to this heading"></a></h3>
+<p>escott requires two files:</p>
+<ul class="simple">
+<li><p>a multiple sequence alignment (MSA) file in fasta format (mandatory):</p></li>
+</ul>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Your</span> <span class="n">query</span> <span class="n">protein</span> <span class="n">must</span> <span class="n">be</span> <span class="n">the</span> <span class="n">first</span> <span class="n">sequence</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">fasta</span> <span class="n">file</span><span class="o">.</span> <span class="n">In</span> <span class="n">addition</span><span class="p">,</span> <span class="n">the</span> <span class="n">query</span> <span class="n">sequence</span> <span class="n">should</span> <span class="ow">not</span> <span class="n">contain</span> <span class="nb">any</span> <span class="n">gaps</span><span class="o">.</span>
+</pre></div>
+</div>
+<ul class="simple">
+<li><p>a structure file in PDB format (optional but highly recommended).</p></li>
+</ul>
+<p>One of the fastest ways to obtain both input MSA and a PDB file is to
+run colabfold:
+<a class="reference external" href="https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb">https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb</a></p>
+<p>Please note that the MSA file produced by colabfold (a3m file) can
+contain gaps in the query sequence. You have to remove them before using
+it in PRESCOTT. You can remove the gaps with pragrams that have a GUI,
+such as ugene (<a class="reference external" href="http://ugene.net/">http://ugene.net/</a>) or jalview (<a class="reference external" href="https://www.jalview.org/">https://www.jalview.org/</a>).</p>
+<p>For testing purpose, you can find some example input files for BLAT
+protein in data/ folder of this repository.</p>
+</section>
+<section id="input-data-requirements-for-prescott">
+<h3>Input Data Requirements for prescott<a class="headerlink" href="#input-data-requirements-for-prescott" title="Permalink to this heading"></a></h3>
+<p>prescott requires three files:</p>
+<ul class="simple">
+<li><p>output file of escott (the file ending with …normPredCombi.txt)</p></li>
+<li><p>a fasta file containing only your query sequence</p></li>
+<li><p>gnomad csv file containing to be downloaded from <a class="reference external" href="https://gnomad.broadinstitute.org/">https://gnomad.broadinstitute.org/</a> for your protein.</p></li>
+</ul>
+</section>
+</section>
+<section id="usage">
+<h2>Usage<a class="headerlink" href="#usage" title="Permalink to this heading"></a></h2>
+<p>You can find example bash scripts for escott and prescott in examples
+folder of this repository.</p>
+<p>Below, you will find examples of the most basic usage. Consult to the
+documentation for further details.</p>
+<section id="running-the-escott-program">
+<h3>Running the escott program<a class="headerlink" href="#running-the-escott-program" title="Permalink to this heading"></a></h3>
+<p>Let’s assume that our input MSA is inputAli.fasta and input.pdb is our
+structure file in PDB format.</p>
+<p>Run the program by issuing the following command in a bash terminal:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott inputAli.fasta -f inputAli.fasta --pdbfile input.pdb
+</pre></div>
+</div>
+<p>A quick help can be accessed by typing</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott --help
+</pre></div>
+</div>
+<p>By default, ESCOTT will predict the effect of all possible single
+mutations at all positions in the query sequence. Alternatively, a set
+of single or multiple mutations can be given with the option -m. Each
+line of the file should contain a mutation (e.g. D136R) or combination
+of mutations separated by colons and ordered according to their
+positions in the sequence (e.g. D136R,V271A).</p>
+</section>
+<section id="running-the-prescott-program">
+<h3>Running the prescott program<a class="headerlink" href="#running-the-prescott-program" title="Permalink to this heading"></a></h3>
+<p>A quick help can be accessed by typing</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>prescott --help
+</pre></div>
+</div>
+<p>Run the program by issuing the following command in a bash terminal:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v2.1.1_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta
+</pre></div>
+</div>
+<p>The most important output is prescott-scores.txt file, which produces
+frequecy modified scores for the mutations.</p>
+<p>Please note that the example input files for prescott are in the data
+directory of this repository.</p>
+</section>
+</section>
+<section id="installation">
+<h2>Installation<a class="headerlink" href="#installation" title="Permalink to this heading"></a></h2>
+<p>PRESCOTT is implemented in Python 3 and R. It has been tested only on
+Linux. Since PRESCOTT has many dependencies, we recommend using our web
+site or our docker image. If you are a determined user, you can find the
+steps required to install it from the source in the following link (or
+in the docs folder of this repository):</p>
+</section>
+<section id="citation">
+<h2>Citation<a class="headerlink" href="#citation" title="Permalink to this heading"></a></h2>
+<p>Coming soon…</p>
+</section>
+</section>
+
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+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
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docs/_build/latex/prescott.aux

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docs/_build/latex/prescott.fdb_latexmk

 # Fdb version 3
-["makeindex prescott.idx"] 1691770116 "prescott.idx" "prescott.ind" "prescott" 1695817598
-  "prescott.idx" 1695817597 0 d41d8cd98f00b204e9800998ecf8427e "pdflatex"
+["makeindex prescott.idx"] 1691770116 "prescott.idx" "prescott.ind" "prescott" 1696926737
+  "prescott.idx" 1696926737 0 d41d8cd98f00b204e9800998ecf8427e "pdflatex"
   (generated)
   "prescott.ilg"
   "prescott.ind"
-["pdflatex"] 1695817597 "prescott.tex" "prescott.pdf" "prescott" 1695817598
+["pdflatex"] 1696926736 "prescott.tex" "prescott.pdf" "prescott" 1696926737
   "/etc/texmf/web2c/texmf.cnf" 1686915816 475 c0e671620eb5563b2130f56340a5fde8 ""
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@@ -140,13 +140,13 @@
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   "/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map" 1692610720 128028 f533b797fba58d231669ea19e894e23e ""
   "/var/lib/texmf/web2c/pdftex/pdflatex.fmt" 1692610730 1455466 cf5d347cc06e6f91065ccb2619b82e95 ""
-  "prescott.aux" 1695817597 6425 d4a0cc942c15d7d060b85f0f9e02b550 "pdflatex"
+  "prescott.aux" 1696926737 8757 49bd9be15e4a1990a75c401ccac48f11 "pdflatex"
   "prescott.ind" 1694694190 0 d41d8cd98f00b204e9800998ecf8427e "makeindex prescott.idx"
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-  "prescott.tex" 1695817596 25850 4bcc5c8c915860158ff9ba881b3f1df9 ""
-  "prescott.toc" 1695817597 1867 651c787e441d7670480cfc3502fbd769 "pdflatex"
+  "prescott.out" 1696926737 6307 8119393c8f110ffbb217a1e7b2c390de "pdflatex"
+  "prescott.tex" 1696926736 31550 20f37acb31b6833dc824f7480aecb279 ""
+  "prescott.toc" 1696926737 2706 6a2a8c488f73b27e9fedb6cddefdfa53 "pdflatex"
   "sphinx.sty" 1691571542 12780 919e6ba449302e2597e7722681a087c6 ""
-  "sphinxhighlight.sty" 1695817596 6679 76d10c62e0f0661410b46f5db6118e26 ""
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@@ -161,7 +161,7 @@
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-  "sphinxmessages.sty" 1695817596 745 3f5fcd6cdd7964ed608767954a8ced6f ""
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   "sphinxpackagefootnote.sty" 1691571543 15217 dd26fe418b6fb1b26b18f042a7f43d40 ""

docs/_build/latex/prescott.fls

@@ -1069,6 +1069,13 @@ INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msam5.tfm
 INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msbm7.tfm
 INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msbm5.tfm
 OUTPUT prescott.toc
+INPUT /usr/share/texmf/fonts/tfm/public/tex-gyre/ec-qtmr.tfm
+INPUT /usr/share/texmf/fonts/tfm/public/tex-gyre/ec-qhvr.tfm
+INPUT /usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
+INPUT /usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
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 []\T1/qtm/m/n/10 Con-grat-u-la-tions! Now, you have all the in-put files re-qui
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docs/_build/latex/prescott.tex

@@ -61,7 +61,7 @@
 
 
 \title{prescott}
-\date{Sep 27, 2023}
+\date{Oct 10, 2023}
 \release{1.5.0}
 \author{Mustafa Tekpinar}
 \newcommand{\sphinxlogo}{\vbox{}}
@@ -85,6 +85,168 @@
 \sphinxstepscope
 
 
+\chapter{Introduction}
+\label{\detokenize{introduction:introduction}}\label{\detokenize{introduction::doc}}
+
+\section{What is PRESCOTT?}
+\label{\detokenize{introduction:what-is-prescott}}
+\sphinxAtStartPar
+PRESCOTT (PRESCOTT: Population awaRe Epistatic and StruCtural mOdel of muTational effecTs) is a package predicting mutational effects in a protein based
+on population, evolutionary and structural information. It is made up of
+two main programs: escott and prescott.
+
+\sphinxAtStartPar
+ESCOTT can calculate effects of single point mutations and multiple
+point mutations. On the other hand, PRESCOTT incorporates population
+frequencies into ESCOTT predictions. Therefore, you need to run ESCOTT
+first to have predictions of mutational effects. We recommend using
+PRESCOTT package via our web site or our docker image due to its
+dependencies.
+
+
+\section{Input Data Requirements}
+\label{\detokenize{introduction:input-data-requirements}}
+
+\subsection{Input Data Requirements for escott}
+\label{\detokenize{introduction:input-data-requirements-for-escott}}
+\sphinxAtStartPar
+escott requires two files:
+\begin{itemize}
+\item {} 
+\sphinxAtStartPar
+a multiple sequence alignment (MSA) file in fasta format (mandatory):
+
+\end{itemize}
+
+\begin{sphinxVerbatim}[commandchars=\\\{\}]
+\PYG{n}{Your} \PYG{n}{query} \PYG{n}{protein} \PYG{n}{must} \PYG{n}{be} \PYG{n}{the} \PYG{n}{first} \PYG{n}{sequence} \PYG{o+ow}{in} \PYG{n}{the} \PYG{n}{fasta} \PYG{n}{file}\PYG{o}{.} \PYG{n}{In} \PYG{n}{addition}\PYG{p}{,} \PYG{n}{the} \PYG{n}{query} \PYG{n}{sequence} \PYG{n}{should} \PYG{o+ow}{not} \PYG{n}{contain} \PYG{n+nb}{any} \PYG{n}{gaps}\PYG{o}{.}
+\end{sphinxVerbatim}
+\begin{itemize}
+\item {} 
+\sphinxAtStartPar
+a structure file in PDB format (optional but highly recommended).
+
+\end{itemize}
+
+\sphinxAtStartPar
+One of the fastest ways to obtain both input MSA and a PDB file is to
+run colabfold:
+\sphinxurl{https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb}
+
+\sphinxAtStartPar
+Please note that the MSA file produced by colabfold (a3m file) can
+contain gaps in the query sequence. You have to remove them before using
+it in PRESCOTT. You can remove the gaps with pragrams that have a GUI,
+such as ugene (\sphinxurl{http://ugene.net/}) or jalview (\sphinxurl{https://www.jalview.org/}).
+
+\sphinxAtStartPar
+For testing purpose, you can find some example input files for BLAT
+protein in data/ folder of this repository.
+
+
+\subsection{Input Data Requirements for prescott}
+\label{\detokenize{introduction:input-data-requirements-for-prescott}}
+\sphinxAtStartPar
+prescott requires three files:
+\begin{itemize}
+\item {} 
+\sphinxAtStartPar
+output file of escott (the file ending with …normPredCombi.txt)
+
+\item {} 
+\sphinxAtStartPar
+a fasta file containing only your query sequence
+
+\item {} 
+\sphinxAtStartPar
+gnomad csv file containing to be downloaded from \sphinxurl{https://gnomad.broadinstitute.org/} for your protein.
+
+\end{itemize}
+
+
+\section{Usage}
+\label{\detokenize{introduction:usage}}
+\sphinxAtStartPar
+You can find example bash scripts for escott and prescott in examples
+folder of this repository.
+
+\sphinxAtStartPar
+Below, you will find examples of the most basic usage. Consult to the
+documentation for further details.
+
+
+\subsection{Running the escott program}
+\label{\detokenize{introduction:running-the-escott-program}}
+\sphinxAtStartPar
+Let’s assume that our input MSA is inputAli.fasta and input.pdb is our
+structure file in PDB format.
+
+\sphinxAtStartPar
+Run the program by issuing the following command in a bash terminal:
+
+\begin{sphinxVerbatim}[commandchars=\\\{\}]
+escott inputAli.fasta \PYGZhy{}f inputAli.fasta \PYGZhy{}\PYGZhy{}pdbfile input.pdb
+\end{sphinxVerbatim}
+
+\sphinxAtStartPar
+A quick help can be accessed by typing
+
+\begin{sphinxVerbatim}[commandchars=\\\{\}]
+escott \PYGZhy{}\PYGZhy{}help
+\end{sphinxVerbatim}
+
+\sphinxAtStartPar
+By default, ESCOTT will predict the effect of all possible single
+mutations at all positions in the query sequence. Alternatively, a set
+of single or multiple mutations can be given with the option \sphinxhyphen{}m. Each
+line of the file should contain a mutation (e.g. D136R) or combination
+of mutations separated by colons and ordered according to their
+positions in the sequence (e.g. D136R,V271A).
+
+
+\subsection{Running the prescott program}
+\label{\detokenize{introduction:running-the-prescott-program}}
+\sphinxAtStartPar
+A quick help can be accessed by typing
+
+\begin{sphinxVerbatim}[commandchars=\\\{\}]
+prescott \PYGZhy{}\PYGZhy{}help
+\end{sphinxVerbatim}
+
+\sphinxAtStartPar
+Run the program by issuing the following command in a bash terminal:
+
+\begin{sphinxVerbatim}[commandchars=\\\{\}]
+prescott \PYGZhy{}e ../data/MLH1\PYGZus{}normPred\PYGZus{}evolCombi.txt \PYGZhy{}g ../data/gnomAD\PYGZus{}v2.1.1\PYGZus{}MLH1\PYGZus{}HUMAN\PYGZus{}ENSG00000076242.csv \PYGZhy{}s ../data/MLH1.fasta
+\end{sphinxVerbatim}
+
+\sphinxAtStartPar
+The most important output is prescott\sphinxhyphen{}scores.txt file, which produces
+frequecy modified scores for the mutations.
+
+\sphinxAtStartPar
+Please note that the example input files for prescott are in the data
+directory of this repository.
+
+
+\section{Installation}
+\label{\detokenize{introduction:installation}}
+\sphinxAtStartPar
+PRESCOTT is implemented in Python 3 and R. It has been tested only on
+Linux. Since PRESCOTT has many dependencies, we recommend using our web
+site or our docker image. If you are a determined user, you can find the
+steps required to install it from the source in the following link (or
+in the docs folder of this repository):
+
+
+\section{Citation}
+\label{\detokenize{introduction:citation}}
+\sphinxAtStartPar
+Coming soon…
+
+\sphinxstepscope
+
+
 \chapter{Using ESCOTT via Docker}
 \label{\detokenize{docker:using-escott-via-docker}}\label{\detokenize{docker::doc}}
 
@@ -258,13 +420,13 @@ mutation and its predicted effect, separated by a space.
 \sphinxstepscope
 
 
-\chapter{Analyzing and Modifying the PRESCOTT Output}
-\label{\detokenize{analysis:analyzing-and-modifying-the-prescott-output}}\label{\detokenize{analysis::doc}}
+\chapter{Analyzing and Modifying the ESCOTT Output}
+\label{\detokenize{analysis:analyzing-and-modifying-the-escott-output}}\label{\detokenize{analysis::doc}}
 
-\section{Raw PRESCOTT Scores and Their Interpretation}
-\label{\detokenize{analysis:raw-prescott-scores-and-their-interpretation}}
+\section{Raw ESCOTT Scores and Their Interpretation}
+\label{\detokenize{analysis:raw-escott-scores-and-their-interpretation}}
 \sphinxAtStartPar
-There is not a hardcoded limit for raw PRESCOTT scores. However, the values
+There is not a hardcoded limit for raw ESCOTT scores. However, the values
 range between {[}\sphinxhyphen{}12, 2{]} generally. The lower values mean the mutations is impactful,
 while values close to 0 means the mutation does not have any significant impact.
 
@@ -276,7 +438,7 @@ it is not always the case.
 \section{Entire Single Point Mutation Landscape Calculations}
 \label{\detokenize{analysis:entire-single-point-mutation-landscape-calculations}}
 \sphinxAtStartPar
-By default, PRESCOTT will only output the combined (independent
+By default, ESCOTT will only output the combined (independent
 and epistatic) scores*:
 
 \sphinxAtStartPar

docs/_build/latex/prescott.toc

 \babel@toc {english}{}\relax 
-\contentsline {chapter}{\numberline {1}Using ESCOTT via Docker}{1}{chapter.1}%
-\contentsline {section}{\numberline {1.1}Requirements}{1}{section.1.1}%
-\contentsline {section}{\numberline {1.2}Getting the example input data}{1}{section.1.2}%
-\contentsline {section}{\numberline {1.3}Single point mutation calculations}{2}{section.1.3}%
-\contentsline {subsection}{\numberline {1.3.1}Obtaining the entire single point mutation landscape}{2}{subsection.1.3.1}%
-\contentsline {subsection}{\numberline {1.3.2}Predicting the effect of a subset of single point mutations}{2}{subsection.1.3.2}%
-\contentsline {section}{\numberline {1.4}Multiple point mutation calculations}{3}{section.1.4}%
-\contentsline {section}{\numberline {1.5}Running several jobs using docker}{3}{section.1.5}%
-\contentsline {chapter}{\numberline {2}Analyzing and Modifying the PRESCOTT Output}{5}{chapter.2}%
-\contentsline {section}{\numberline {2.1}Raw PRESCOTT Scores and Their Interpretation}{5}{section.2.1}%
-\contentsline {section}{\numberline {2.2}Entire Single Point Mutation Landscape Calculations}{5}{section.2.2}%
-\contentsline {section}{\numberline {2.3}Selected Single Point or Multiple Point Mutation Calculations}{6}{section.2.3}%
-\contentsline {chapter}{\numberline {3}Preparing Your Own Input}{7}{chapter.3}%
-\contentsline {section}{\numberline {3.1}Preparing Your Input MSA and PDB with Colabfold}{7}{section.3.1}%
-\contentsline {chapter}{\numberline {4}Installation}{9}{chapter.4}%
-\contentsline {section}{\numberline {4.1}Installing the dependencies:}{9}{section.4.1}%
-\contentsline {section}{\numberline {4.2}Preparation of the environment and installation of PRESCOTT}{9}{section.4.2}%
-\contentsline {section}{\numberline {4.3}Configuring default.conf file}{11}{section.4.3}%
-\contentsline {chapter}{\numberline {5}Indices and tables}{13}{chapter.5}%
+\contentsline {chapter}{\numberline {1}Introduction}{1}{chapter.1}%
+\contentsline {section}{\numberline {1.1}What is PRESCOTT?}{1}{section.1.1}%
+\contentsline {section}{\numberline {1.2}Input Data Requirements}{1}{section.1.2}%
+\contentsline {subsection}{\numberline {1.2.1}Input Data Requirements for escott}{1}{subsection.1.2.1}%
+\contentsline {subsection}{\numberline {1.2.2}Input Data Requirements for prescott}{2}{subsection.1.2.2}%
+\contentsline {section}{\numberline {1.3}Usage}{2}{section.1.3}%
+\contentsline {subsection}{\numberline {1.3.1}Running the escott program}{2}{subsection.1.3.1}%
+\contentsline {subsection}{\numberline {1.3.2}Running the prescott program}{2}{subsection.1.3.2}%
+\contentsline {section}{\numberline {1.4}Installation}{3}{section.1.4}%
+\contentsline {section}{\numberline {1.5}Citation}{3}{section.1.5}%
+\contentsline {chapter}{\numberline {2}Using ESCOTT via Docker}{5}{chapter.2}%
+\contentsline {section}{\numberline {2.1}Requirements}{5}{section.2.1}%
+\contentsline {section}{\numberline {2.2}Getting the example input data}{5}{section.2.2}%
+\contentsline {section}{\numberline {2.3}Single point mutation calculations}{6}{section.2.3}%
+\contentsline {subsection}{\numberline {2.3.1}Obtaining the entire single point mutation landscape}{6}{subsection.2.3.1}%
+\contentsline {subsection}{\numberline {2.3.2}Predicting the effect of a subset of single point mutations}{6}{subsection.2.3.2}%
+\contentsline {section}{\numberline {2.4}Multiple point mutation calculations}{7}{section.2.4}%
+\contentsline {section}{\numberline {2.5}Running several jobs using docker}{7}{section.2.5}%
+\contentsline {chapter}{\numberline {3}Analyzing and Modifying the ESCOTT Output}{9}{chapter.3}%
+\contentsline {section}{\numberline {3.1}Raw ESCOTT Scores and Their Interpretation}{9}{section.3.1}%
+\contentsline {section}{\numberline {3.2}Entire Single Point Mutation Landscape Calculations}{9}{section.3.2}%
+\contentsline {section}{\numberline {3.3}Selected Single Point or Multiple Point Mutation Calculations}{10}{section.3.3}%
+\contentsline {chapter}{\numberline {4}Preparing Your Own Input}{11}{chapter.4}%
+\contentsline {section}{\numberline {4.1}Preparing Your Input MSA and PDB with Colabfold}{11}{section.4.1}%
+\contentsline {chapter}{\numberline {5}Installation}{13}{chapter.5}%
+\contentsline {section}{\numberline {5.1}Installing the dependencies:}{13}{section.5.1}%
+\contentsline {section}{\numberline {5.2}Preparation of the environment and installation of PRESCOTT}{13}{section.5.2}%
+\contentsline {section}{\numberline {5.3}Configuring default.conf file}{15}{section.5.3}%
+\contentsline {chapter}{\numberline {6}Indices and tables}{17}{chapter.6}%

docs/analysis.rst

-Analyzing and Modifying the PRESCOTT Output
+Analyzing and Modifying the ESCOTT Output
 ==========================================
 
-Raw PRESCOTT Scores and Their Interpretation
+Raw ESCOTT Scores and Their Interpretation
 -------------------------------------------
-There is not a hardcoded limit for raw PRESCOTT scores. However, the values
+There is not a hardcoded limit for raw ESCOTT scores. However, the values
 range between [-12, 2] generally. The lower values mean the mutations is impactful, 
 while values close to 0 means the mutation does not have any significant impact.
 
@@ -13,7 +13,7 @@ it is not always the case.
 Entire Single Point Mutation Landscape Calculations
 ---------------------------------------------------
 
-By default, PRESCOTT will only output the combined (independent
+By default, ESCOTT will only output the combined (independent
 and epistatic) scores*: 
 
 There are three output files:

docs/index.rst

-.. esgemme documentation master file, created by
+.. PRESCOTT documentation master file, created by
    sphinx-quickstart on Fri May  5 13:52:13 2023.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to esgemme's documentation!
+Welcome to PRESCOTT documentation!
 ===================================
 
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
 
+   introduction.rst
    docker.rst
    analysis.rst
    input-preparation.rst

docs/introduction.rst

+
+Introduction
+============
+What is PRESCOTT?
+-----------------
+
+PRESCOTT (PRESCOTT: Population awaRe Epistatic and StruCtural mOdel of muTational effecTs) is a package predicting mutational effects in a protein based
+on population, evolutionary and structural information. It is made up of
+two main programs: escott and prescott.
+
+ESCOTT can calculate effects of single point mutations and multiple
+point mutations. On the other hand, PRESCOTT incorporates population
+frequencies into ESCOTT predictions. Therefore, you need to run ESCOTT
+first to have predictions of mutational effects. We recommend using
+PRESCOTT package via our web site or our docker image due to its
+dependencies.
+
+Input Data Requirements
+-----------------------
+
+Input Data Requirements for escott
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+escott requires two files:
+
+* a multiple sequence alignment (MSA) file in fasta format (mandatory):
+
+::
+
+   Your query protein must be the first sequence in the fasta file. In addition, the query sequence should not contain any gaps. 
+
+
+* a structure file in PDB format (optional but highly recommended).
+
+One of the fastest ways to obtain both input MSA and a PDB file is to
+run colabfold:
+https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb
+
+Please note that the MSA file produced by colabfold (a3m file) can
+contain gaps in the query sequence. You have to remove them before using
+it in PRESCOTT. You can remove the gaps with pragrams that have a GUI,
+such as ugene (http://ugene.net/) or jalview (https://www.jalview.org/).
+
+For testing purpose, you can find some example input files for BLAT
+protein in data/ folder of this repository. 
+
+Input Data Requirements for prescott
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+prescott requires three files:
+
+* output file of escott (the file ending with …normPredCombi.txt) 
+* a fasta file containing only your query sequence 
+* gnomad csv file containing to be downloaded from https://gnomad.broadinstitute.org/ for your protein.
+
+Usage
+-----
+
+You can find example bash scripts for escott and prescott in examples
+folder of this repository.
+
+Below, you will find examples of the most basic usage. Consult to the
+documentation for further details.
+
+Running the escott program
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Let’s assume that our input MSA is inputAli.fasta and input.pdb is our
+structure file in PDB format.
+
+Run the program by issuing the following command in a bash terminal:
+
+.. code:: bash
+
+   escott inputAli.fasta -f inputAli.fasta --pdbfile input.pdb 
+
+A quick help can be accessed by typing
+
+.. code:: bash
+
+   escott --help
+
+By default, ESCOTT will predict the effect of all possible single
+mutations at all positions in the query sequence. Alternatively, a set
+of single or multiple mutations can be given with the option -m. Each
+line of the file should contain a mutation (e.g. D136R) or combination
+of mutations separated by colons and ordered according to their
+positions in the sequence (e.g. D136R,V271A).
+
+Running the prescott program
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+A quick help can be accessed by typing
+
+.. code:: bash
+
+   prescott --help
+
+Run the program by issuing the following command in a bash terminal:
+
+.. code:: bash
+
+   prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v2.1.1_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta 
+
+The most important output is prescott-scores.txt file, which produces
+frequecy modified scores for the mutations.
+
+Please note that the example input files for prescott are in the data
+directory of this repository.
+
+Installation
+------------
+
+PRESCOTT is implemented in Python 3 and R. It has been tested only on
+Linux. Since PRESCOTT has many dependencies, we recommend using our web
+site or our docker image. If you are a determined user, you can find the
+steps required to install it from the source in the following link (or
+in the docs folder of this repository):
+
+Citation
+--------
+
+Coming soon…
+
+.. |License: MIT| image:: https://img.shields.io/badge/License-MIT-yellow.svg
+   :target: https://opensource.org/licenses/MIT
+