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ehmmbuild |
% ehmmbuild globins50.msf globin.hmm -auto hmmbuild - build a hidden Markov model from an alignment HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Training alignment: ../../data/hmm/globins50.msf Number of sequences: 50 Search algorithm configuration: Local (hmmsw) S/W aggregate entry probability: 0.50 S/W aggregate exit probability: 0.50 Model construction strategy: Fast/ad hoc (gapmax 0.50) Null model used: (default) Prior used: (default) Prior strategy: Dirichlet Sequence weighting method: G/S/C tree weights - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Determining effective sequence number ... done. [14] Weighting sequences heuristically ... done. Constructing model architecture ... done. Saving count vector file ... done. [globins50.out3] Converting counts to probabilities ... done. Setting model name, etc. ... done. [globins50] Constructed a profile HMM (length 146) Average score: 187.26 bits Minimum score: 77.42 bits Maximum score: 248.11 bits Std. deviation: 47.00 bits Finalizing model configuration ... done. Saving model to file ... done. [globin.hmm] Saving annotated alignment ... done. [globins50.out2] |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers: [-sequences] seqset Sequence set USA [-outfile] outfile Output file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -priorfile infile Dirichlet prior file -nullfile infile NULL model file -pamfile infile PAM file -strategy menu Select preference -append boolean Append to file -amino boolean Treat as protein -nucleic boolean Treat as dna -archpri float Architecture prior -binary boolean Write HMM as binary -cstrategy menu Select strategy -fast boolean Work in fast mode -gapmax float Fast mode control -hand boolean Specify model by hand -idlevel float Cutoff ID threhold -[no]efficiency boolean Be efficient -pamweight float Weighting for PAM -swentry float Probability control for local entries -swexit float Probability control for exits -more boolean Verbosity -weighting menu Select weighting -resavefile outfile Resave selex filename -cfile outfile Emission and transition count file Associated qualifiers: "-sequences" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outfile" associated qualifiers -odirectory2 string Output directory "-resavefile" associated qualifiers -odirectory string Output directory "-cfile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
[-sequences] (Parameter 1) |
Sequence set USA | Readable set of sequences | Required | ||||||||||
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.ehmmbuild | ||||||||||
Additional (Optional) qualifiers | Allowed values | Default | |||||||||||
(none) | |||||||||||||
Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||||
-priorfile | Dirichlet prior file | Input file | Required | ||||||||||
-nullfile | NULL model file | Input file | Required | ||||||||||
-pamfile | PAM file | Input file | Required | ||||||||||
-strategy | Select preference |
|
L | ||||||||||
-append | Append to file | Boolean value Yes/No | No | ||||||||||
-amino | Treat as protein | Boolean value Yes/No | No | ||||||||||
-nucleic | Treat as dna | Boolean value Yes/No | No | ||||||||||
-archpri | Architecture prior | Any numeric value | 0.85 | ||||||||||
-binary | Write HMM as binary | Boolean value Yes/No | No | ||||||||||
-cstrategy | Select strategy |
|
F | ||||||||||
-fast | Work in fast mode | Boolean value Yes/No | No | ||||||||||
-gapmax | Fast mode control | Any numeric value | 0.5 | ||||||||||
-hand | Specify model by hand | Boolean value Yes/No | No | ||||||||||
-idlevel | Cutoff ID threhold | Any numeric value | 0.62 | ||||||||||
-[no]efficiency | Be efficient | Boolean value Yes/No | Yes | ||||||||||
-pamweight | Weighting for PAM | Any numeric value | 20.0 | ||||||||||
-swentry | Probability control for local entries | Any numeric value | 0.5 | ||||||||||
-swexit | Probability control for exits | Any numeric value | 0.5 | ||||||||||
-more | Verbosity | Boolean value Yes/No | No | ||||||||||
-weighting | Select weighting |
|
G | ||||||||||
-resavefile | Resave selex filename | Output file | |||||||||||
-cfile | Emission and transition count file | Output file |
MSF: 171 Type: P Check: 4694 .. Name: GLB2_MORMR oo Len: 171 Check: 6522 Weight: 2.7687 Name: GLBZ_CHITH oo Len: 171 Check: 6733 Weight: 2.9329 Name: HBA2_BOSMU oo Len: 171 Check: 5006 Weight: 0.6394 Name: HBA2_GALCR oo Len: 171 Check: 6652 Weight: 0.5183 Name: HBA4_SALIR oo Len: 171 Check: 5434 Weight: 1.9511 Name: HBAD_CHLME oo Len: 171 Check: 6621 Weight: 1.2927 Name: HBAD_PASMO oo Len: 171 Check: 8118 Weight: 1.2927 Name: HBAZ_HORSE oo Len: 171 Check: 8382 Weight: 1.6223 Name: HBA_AILME oo Len: 171 Check: 5402 Weight: 0.4145 Name: HBA_ANSSE oo Len: 171 Check: 3688 Weight: 0.8315 Name: HBA_COLLI oo Len: 171 Check: 4420 Weight: 0.8557 Name: HBA_ERIEU oo Len: 171 Check: 5528 Weight: 0.8390 Name: HBA_FRAPO oo Len: 171 Check: 4136 Weight: 0.5014 Name: HBA_MACFA oo Len: 171 Check: 5986 Weight: 0.2233 Name: HBA_MACSI oo Len: 171 Check: 6064 Weight: 0.2233 Name: HBA_MESAU oo Len: 171 Check: 5499 Weight: 0.6722 Name: HBA_PAGLA oo Len: 171 Check: 6189 Weight: 0.5388 Name: HBA_PHACO oo Len: 171 Check: 5129 Weight: 0.5014 Name: HBA_PONPY oo Len: 171 Check: 5894 Weight: 0.3907 Name: HBA_PROLO oo Len: 171 Check: 5810 Weight: 0.4145 Name: HBA_TRIOC oo Len: 171 Check: 6427 Weight: 0.6883 Name: HBB1_VAREX oo Len: 171 Check: 7239 Weight: 1.1252 Name: HBB2_TRICR oo Len: 171 Check: 7790 Weight: 1.9629 Name: HBB2_XENTR oo Len: 171 Check: 9537 Weight: 1.4685 Name: HBBL_RANCA oo Len: 171 Check: 7490 Weight: 1.4685 Name: HBB_CALAR oo Len: 171 Check: 6568 Weight: 0.4226 Name: HBB_COLLI oo Len: 171 Check: 5043 Weight: 0.7672 Name: HBB_EQUHE oo Len: 171 Check: 6101 Weight: 0.6734 Name: HBB_LARRI oo Len: 171 Check: 5673 Weight: 0.7672 Name: HBB_MANSP oo Len: 171 Check: 7148 Weight: 0.4226 Name: HBB_ORNAN oo Len: 171 Check: 6249 Weight: 0.6615 Name: HBB_RABIT oo Len: 171 Check: 7043 Weight: 0.5259 Name: HBB_SPECI oo Len: 171 Check: 3680 Weight: 0.5422 Name: HBB_SPETO oo Len: 171 Check: 4246 Weight: 0.5422 Name: HBB_SUNMU oo Len: 171 Check: 5601 Weight: 0.6734 Name: HBB_TACAC oo Len: 171 Check: 7133 Weight: 0.6615 Name: HBB_TRIIN oo Len: 171 Check: 4009 Weight: 0.8445 Name: HBB_TUPGL oo Len: 171 Check: 7197 Weight: 0.7375 Name: HBB_URSMA oo Len: 171 Check: 7200 Weight: 0.4695 Name: HBE_PONPY oo Len: 171 Check: 5902 Weight: 1.0101 Name: HBF1_URECA oo Len: 171 Check: 6462 Weight: 2.9329 Name: LGB1_PEA oo Len: 171 Check: 4791 Weight: 2.0005 Name: LGB1_VICFA oo Len: 171 Check: 7426 Weight: 2.0005 Name: MYG_ESCGI oo Len: 171 Check: 9170 Weight: 0.7432 Name: MYG_HORSE oo Len: 171 Check: 1290 Weight: 0.7432 Name: MYG_LYCPI oo Len: 171 Check: 1107 Weight: 0.8773 [Part of this file has been deleted for brevity] GLB2_MORMR KLMSMICILL SSAY...... . GLBZ_CHITH ATFDAFFGAV FAK....... M HBA2_BOSMU KFLANVSTVL TSKYR..... . HBA2_GALCR KFMASVSTVL TSKYR..... . HBA4_SALIR KFLQQLALAL AEKYR..... . HBAD_CHLME KFLSAVAAVL AEKYR..... . HBAD_PASMO KFMSAVASVL AEKYR..... . HBAZ_HORSE KFLSIVSSVL TEKYR..... . HBA_AILME KFFSAVSTVL TSKYR..... . HBA_ANSSE KFLCAVATVL TAKYR..... . HBA_COLLI KFVLAVGTVL TAKYR..... . HBA_ERIEU KFLATVATVL TSKYR..... . HBA_FRAPO KFLCAVGNVL TAKYR..... . HBA_MACFA KFLASVSTVL TSKYR..... . HBA_MACSI KFLASVSTVL TSKYR..... . HBA_MESAU KFFASVSTVL TSKYR..... . HBA_PAGLA KFFSAVSTVL TSKYR..... . HBA_PHACO KFLCAVGTVL TAKYR..... . HBA_PONPY KFLASVSTVL TSKYR..... . HBA_PROLO KFFTSVSTVL TSKYR..... . HBA_TRIOC KFLCAVGNVL SAKYR..... . HBB1_VAREX KLVNVVSHSL ARRYH..... . HBB2_TRICR KLMKGVSHAL GHGY...... . HBB2_XENTR KLNATLVAAL SHGYF..... . HBBL_RANCA KFIAVLVDAL SHSYH..... . HBB_CALAR KVVAGVANAL AHKYH..... . HBB_COLLI KLVRVVAHAL ARKYH..... . HBB_EQUHE KVVAGVANAL AHKYH..... . HBB_LARRI KLVRVVAHAL ARKYH..... . HBB_MANSP KVVAGVANAL AHKYH..... . HBB_ORNAN KLVSGVAHAL GHKYH..... . HBB_RABIT KVVAGVANAL AHKYH..... . HBB_SPECI KVVAGVANAL AHKYH..... . HBB_SPETO KVVAGVANAL SHKYH..... . HBB_SUNMU KVVAGVANAL AHKYH..... . HBB_TACAC KLVSGVSHAL AHKYH..... . HBB_TRIIN KVVAGVANAL AHKYH..... . HBB_TUPGL KVVAGVANAL AHKYH..... . HBB_URSMA KVVAGVANAL AHKYH..... . HBE_PONPY KLVSAVAIAL AHKYH..... . HBF1_URECA DAAGVLVAAM .......... K LGB1_PEA VAYDGLATAI KKAMKT.... A LGB1_VICFA VAYDGLATAI K....A.... A MYG_ESCGI KALELFRKDI AAKYKELGFQ G MYG_HORSE KALELFRNDI AAKYKELGFQ G MYG_LYCPI KALELFRNDI AAKYKELGFQ G MYG_MOUSE KALELFRNDI AAKYKELGFQ G MYG_MUSAN GAFKIICSDI EKEYKAANFQ G MYG_PROGU KALELFRNDI AAKYKELGFQ G MYG_SAISC KALELFRNDM AAKYKELGFQ G |
HMMER2.0 NAME globins50 LENG 146 ALPH Amino RF no CS no MAP yes COM ehmmbuild ../../data/hmm/globins50.msf globin.hmm -auto NSEQ 50 DATE Fri Feb 18 10:17:03 2005 CKSUM 5854 XT -8455 -4 0 * -8455 -4 0 * NULT -4 -8455 NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 HMM A C D E F G H I K L M N P Q R S T V W Y m->m m->i m->d i->m i->i d->m d->d b->m m->e -93 * -4000 1 -1967 -2271 -4498 -4217 -3055 1639 -3307 -2518 -3920 -2945 2068 -3352 193 -3569 -3796 257 -2222 2801 -3514 -3205 1 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -9 -9065 -10107 -894 -1115 -701 -1378 -1093 -8180 2 -1670 -1776 -76 -2279 1025 -3037 3194 232 -52 1914 -955 -2245 -3102 -1004 -2223 -2065 -1610 -1207 -2178 -1775 2 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -9 -9065 -10107 -894 -1115 -701 -1378 -8273 -8175 3 -1713 -1550 -3992 -3365 801 -3249 -2111 -1027 -2974 762 -736 -2876 -3301 -2606 -2796 1725 1747 269 3309 -1618 3 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -9 -9065 -10107 -894 -1115 -701 -1378 -8273 -8170 4 1140 -2941 1606 792 -3253 -2463 -1127 -278 -63 -2954 -2034 -1102 -473 -671 -1220 572 1661 -2558 -3131 -2454 4 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -9 -9065 -10107 -894 -1115 -701 -1378 -8273 -8165 5 1794 -2944 -65 -235 -3261 829 -1114 -284 1649 -2958 -2034 -134 -1104 -656 -1204 60 -589 -2564 -3130 -2449 5 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -9 -9065 -10107 -894 -1115 -701 -1378 -8273 -8160 6 -1748 -3220 1958 2253 -3519 172 -1355 -3271 -993 -829 -2323 -1243 -2761 1731 -1518 -1165 -1696 -335 -3410 -2713 6 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -9 -9065 -10107 -894 -1115 -701 -1378 -8273 -8155 7 -173 -2945 -205 2098 -3264 -2452 -1111 -302 1817 -2960 -2035 433 -2545 -652 -261 -62 -1417 -2566 2430 -2449 7 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -9 -9065 -10107 -894 -1115 -701 -1378 -8273 -8150 8 933 -2910 -1344 -795 -3214 -1181 -1120 -2952 2227 -837 -2004 -157 -2553 1184 -129 241 381 -316 -3104 -2432 8 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -9 -9065 -10107 -894 -1115 -701 -1378 -8273 -8145 9 1054 1483 -2717 -2142 -1752 -2967 -1753 -661 -506 965 533 1919 -3033 494 -2159 300 -763 120 -2182 -1788 9 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -9 -9065 -10107 -894 -1115 -701 -1378 -8273 -8140 10 475 -184 -3984 -927 -1458 -3217 -2087 964 -2953 185 -705 -2852 14 -2583 -2766 -2300 -535 2595 1896 -1619 10 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -9 -9065 -10107 -894 -1115 -701 -1378 -8273 -8134 11 -171 -2034 -2133 -1572 -2075 -2788 -1524 1191 1414 546 -1206 859 -2865 894 -1789 -14 -603 1034 -2415 -1962 11 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -9 -9065 -10107 -894 -1115 -701 -1378 -8273 -8129 [Part of this file has been deleted for brevity] - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -13 -9069 -10111 -894 -1115 -701 -1378 -8273 -7331 131 1046 -2920 936 659 -3228 -2456 -1116 -1039 363 -2931 1609 -673 -2549 2249 -1206 -311 -848 236 -3111 -2436 131 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -13 -9069 -10111 -894 -1115 -701 -1378 -8273 -7322 132 1525 -2380 -1743 -1189 -2505 -2643 -1343 -80 2077 -2311 -1534 -729 -2731 501 -1500 -603 -889 1459 -2705 -2176 132 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -13 -9069 -10111 -894 -1115 -701 -1378 -8273 -7313 133 738 -1513 -3848 -3222 -198 361 -2054 325 428 1007 -714 -2784 -3243 -2505 -2708 324 -1602 1238 -1968 1351 133 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -13 -9069 -10111 -894 -1115 -701 -1378 -8273 -7304 134 987 1437 598 -22 375 -425 -1546 -562 -1482 -1887 629 128 -2881 -1372 -1826 -262 958 1290 -2386 -1941 134 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -13 -9069 -10111 -894 -1115 -701 -1378 -8273 -7295 135 1231 -2587 -1541 216 -2769 193 -1233 -2428 -54 355 -1715 -467 -2642 -839 -418 386 -1448 1716 -2861 -2275 135 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -13 -9069 -10111 -894 -1115 -701 -1378 -8273 -7285 136 606 -2680 165 660 -2889 865 -1213 -2564 326 1588 -1802 -1227 -2627 -803 -1338 -1459 -507 11 -2936 -2329 136 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -13 -9069 -10111 -894 -1115 -701 -1378 -8273 -7276 137 804 -1523 -4031 -3398 -1482 -3248 -2124 348 -2998 1327 -725 -2891 -3297 -2625 -2804 -1588 1321 1922 1901 -1649 137 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -13 -9069 -10111 -894 -1115 -701 -1378 -8273 -7267 138 1808 -1941 -2321 901 973 -408 -1613 -1543 -1607 -1831 1197 -1869 -2928 -1483 -1921 869 632 -3 -2347 -1916 138 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -13 -9069 -10111 -894 -1115 -701 -1378 -8273 -7257 139 1340 -2950 -394 203 -3271 -2451 1896 -1633 1977 -2966 -2040 1016 -2545 -650 779 -62 -1417 -2572 -3134 -2451 139 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -13 -9069 -10111 -894 -1115 -701 -1378 -8273 -7248 140 1476 -2348 -1739 120 -2460 -2637 -1336 497 345 -2272 1946 710 -2722 -1006 -1512 -916 102 -1854 -2672 2397 140 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -14 -9069 -10111 -894 -1115 -701 -1378 -8273 -7238 141 -1642 -1910 588 -1926 393 -2933 -1677 165 1129 1319 -1086 -1997 -3002 -1605 1807 -1932 -1580 -1356 -2286 1485 141 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -15 -8608 -9650 -894 -1115 -701 -1378 -8273 -7229 142 1542 1691 488 -582 -2626 -279 -862 506 1171 -2375 -136 -872 -2282 -440 468 312 -1114 -1970 -2642 -2022 142 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -16 -8505 -9547 -894 -1115 -701 -1378 -8273 -7219 143 2278 -2091 -2495 -1900 -2272 -2771 3583 522 -1069 -2122 -1438 -1912 -2941 -1387 524 -1886 -1664 -1689 -2531 -2110 143 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -16 -8405 -9447 -894 -1115 -701 -1378 -8273 -7209 144 1313 -1624 -1590 -1030 784 176 -1023 -1263 1746 -28 1368 -1204 -2374 -799 -322 -323 -1039 -1096 -1996 -1532 144 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -16 -8405 -9447 -894 -1115 -701 -1378 -8273 -7200 145 -2395 -2460 -3209 -2720 1335 -3543 -1417 -2096 1716 53 -1668 854 -3574 -2202 -2474 -2599 -2321 -2018 -1148 3600 145 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -17 -8323 -9365 -894 -1115 -701 -1378 -8273 -7190 146 -1328 -1570 -2202 -1667 1530 183 3522 -1184 -1501 -1451 -788 -1688 -2680 -1341 -1757 347 444 -1057 -1556 1992 146 - * * * * * * * * * * * * * * * * * * * * - * * * * * * * -8273 0 // |
#=AU HMMER 2.1.1 #=SQ GLB2_MORMR 0.8470 - - 0..0::0 - #=SQ GLBZ_CHITH 0.8239 - - 0..0::0 - #=SQ HBA2_BOSMU 0.1489 - - 0..0::0 - #=SQ HBA2_GALCR 0.1303 - - 0..0::0 - #=SQ HBA4_SALIR 0.7409 - - 0..0::0 - #=SQ HBAD_CHLME 0.3489 - - 0..0::0 - #=SQ HBAD_PASMO 0.3489 - - 0..0::0 - #=SQ HBAZ_HORSE 0.4248 - - 0..0::0 - #=SQ HBA_AILME 0.1053 - - 0..0::0 - #=SQ HBA_ANSSE 0.2171 - - 0..0::0 - #=SQ HBA_COLLI 0.2295 - - 0..0::0 - #=SQ HBA_ERIEU 0.2144 - - 0..0::0 - #=SQ HBA_FRAPO 0.1349 - - 0..0::0 - #=SQ HBA_MACFA 0.0579 - - 0..0::0 - #=SQ HBA_MACSI 0.0579 - - 0..0::0 - #=SQ HBA_MESAU 0.1698 - - 0..0::0 - #=SQ HBA_PAGLA 0.1330 - - 0..0::0 - #=SQ HBA_PHACO 0.1349 - - 0..0::0 - #=SQ HBA_PONPY 0.1013 - - 0..0::0 - #=SQ HBA_PROLO 0.1053 - - 0..0::0 - #=SQ HBA_TRIOC 0.1834 - - 0..0::0 - #=SQ HBB1_VAREX 0.2835 - - 0..0::0 - #=SQ HBB2_TRICR 0.5133 - - 0..0::0 - #=SQ HBB2_XENTR 0.3959 - - 0..0::0 - #=SQ HBBL_RANCA 0.3959 - - 0..0::0 - #=SQ HBB_CALAR 0.1102 - - 0..0::0 - #=SQ HBB_COLLI 0.1890 - - 0..0::0 - #=SQ HBB_EQUHE 0.1760 - - 0..0::0 - #=SQ HBB_LARRI 0.1890 - - 0..0::0 - #=SQ HBB_MANSP 0.1102 - - 0..0::0 - #=SQ HBB_ORNAN 0.1667 - - 0..0::0 - #=SQ HBB_RABIT 0.1265 - - 0..0::0 - #=SQ HBB_SPECI 0.1303 - - 0..0::0 - #=SQ HBB_SPETO 0.1303 - - 0..0::0 - #=SQ HBB_SUNMU 0.1699 - - 0..0::0 - #=SQ HBB_TACAC 0.1667 - - 0..0::0 - #=SQ HBB_TRIIN 0.1889 - - 0..0::0 - #=SQ HBB_TUPGL 0.1889 - - 0..0::0 - #=SQ HBB_URSMA 0.1202 - - 0..0::0 - #=SQ HBE_PONPY 0.2359 - - 0..0::0 - #=SQ HBF1_URECA 0.8135 - - 0..0::0 - #=SQ LGB1_PEA 0.6773 - - 0..0::0 - #=SQ LGB1_VICFA 0.6773 - - 0..0::0 - #=SQ MYG_ESCGI 0.2107 - - 0..0::0 - #=SQ MYG_HORSE 0.2107 - - 0..0::0 - #=SQ MYG_LYCPI 0.2542 - - 0..0::0 - #=SQ MYG_MOUSE 0.2542 - - 0..0::0 - #=SQ MYG_MUSAN 0.8232 - - 0..0::0 - #=SQ MYG_PROGU 0.2168 - - 0..0::0 - [Part of this file has been deleted for brevity] GLB2_MORMR ... GLBZ_CHITH km. HBA2_BOSMU ... HBA2_GALCR ... HBA4_SALIR ... HBAD_CHLME ... HBAD_PASMO ... HBAZ_HORSE ... HBA_AILME ... HBA_ANSSE ... HBA_COLLI ... HBA_ERIEU ... HBA_FRAPO ... HBA_MACFA ... HBA_MACSI ... HBA_MESAU ... HBA_PAGLA ... HBA_PHACO ... HBA_PONPY ... HBA_PROLO ... HBA_TRIOC ... HBB1_VAREX ... HBB2_TRICR ... HBB2_XENTR ... HBBL_RANCA ... HBB_CALAR ... HBB_COLLI ... HBB_EQUHE ... HBB_LARRI ... HBB_MANSP ... HBB_ORNAN ... HBB_RABIT ... HBB_SPECI ... HBB_SPETO ... HBB_SUNMU ... HBB_TACAC ... HBB_TRIIN ... HBB_TUPGL ... HBB_URSMA ... HBE_PONPY ... HBF1_URECA ... LGB1_PEA ... LGB1_VICFA ... MYG_ESCGI fqg MYG_HORSE fqg MYG_LYCPI fqg MYG_MOUSE fqg MYG_MUSAN ... MYG_PROGU fqg MYG_SAISC fqg |
M 0.00 0.00 0.00 0.00 0.00 3.32 0.00 0.00 0.00 0.00 1.52 0.00 0.85 0.00 0.00 1.17 0.00 7.14 0.00 0.00 M 0.00 0.00 0.82 0.00 1.35 0.00 3.81 0.85 0.82 6.16 0.00 0.00 0.00 0.18 0.00 0.00 0.00 0.00 0.00 0.00 M 0.00 0.00 0.00 0.00 1.06 0.00 0.00 0.00 0.00 2.30 0.00 0.00 0.00 0.00 0.00 4.23 3.29 0.85 2.28 0.00 M 2.87 0.00 2.89 1.50 0.00 0.00 0.00 0.82 0.42 0.00 0.00 0.00 0.56 0.00 0.00 1.64 3.30 0.00 0.00 0.00 M 4.85 0.00 0.61 0.35 0.00 2.25 0.00 0.82 3.09 0.00 0.00 0.41 0.30 0.00 0.00 0.97 0.34 0.00 0.00 0.00 M 0.00 0.00 3.56 5.18 0.00 1.27 0.00 0.00 0.00 0.82 0.00 0.00 0.00 2.17 0.00 0.17 0.00 0.82 0.00 0.00 M 0.82 0.00 0.51 4.83 0.00 0.00 0.00 0.81 3.56 0.00 0.00 0.82 0.00 0.00 0.42 0.85 0.00 0.00 1.36 0.00 M 2.42 0.00 0.00 0.00 0.00 0.37 0.00 0.00 4.99 0.82 0.00 0.40 0.00 1.36 0.51 1.18 1.10 0.85 0.00 0.00 M 2.56 0.82 0.00 0.00 0.00 0.00 0.00 0.25 0.51 2.95 0.42 3.13 0.00 0.87 0.00 1.37 0.28 0.82 0.00 0.00 M 1.54 0.17 0.00 0.51 0.00 0.00 0.00 1.57 0.00 1.32 0.00 0.00 0.85 0.00 0.00 0.00 0.40 6.82 0.82 0.00 M 0.82 0.00 0.00 0.00 0.00 0.00 0.00 2.23 2.69 2.21 0.00 1.35 0.00 1.16 0.00 0.99 0.35 2.18 0.00 0.00 M 4.21 0.28 0.87 0.17 0.00 0.27 0.00 0.19 0.00 0.18 0.00 1.76 0.00 0.70 0.00 2.89 2.49 0.00 0.00 0.00 M 2.42 0.00 0.85 0.00 0.21 0.86 0.81 2.47 0.00 0.35 0.00 0.33 0.00 0.00 0.00 2.85 0.71 2.13 0.00 0.00 M 1.11 0.00 0.00 0.82 0.90 0.00 0.00 0.70 0.00 2.23 0.00 0.00 0.00 0.00 0.00 2.18 0.00 0.79 5.26 0.00 M 1.26 0.00 0.34 2.00 0.81 3.77 0.00 0.00 0.00 0.51 0.00 0.00 0.00 0.68 0.00 0.82 0.32 0.00 3.47 0.00 M 0.19 0.00 1.00 0.00 0.68 2.99 0.00 0.00 6.20 2.31 0.00 0.00 0.00 0.40 0.00 0.24 0.00 0.00 0.00 0.00 M 0.00 0.00 0.00 0.00 0.68 0.00 0.17 2.58 4.50 1.39 0.00 1.66 0.00 0.00 0.00 0.82 0.00 2.21 0.00 0.00 M 0.48 0.00 0.00 1.36 0.00 2.84 0.00 1.10 1.52 0.74 0.24 0.00 0.00 0.68 0.00 0.56 1.01 3.47 0.00 0.00 M 1.95 0.00 2.09 0.00 0.00 2.54 0.13 0.85 0.81 0.00 0.42 3.27 0.74 0.68 0.00 0.27 0.25 0.00 0.00 0.00 M 0.61 0.00 1.36 0.35 0.00 0.81 2.24 1.39 0.74 0.87 0.00 0.68 0.00 1.48 0.85 0.00 0.00 2.63 0.00 0.00 M 3.82 0.81 1.02 1.87 0.00 1.32 0.00 1.25 0.19 0.73 0.00 0.33 1.35 0.35 0.00 0.74 0.00 0.21 0.00 0.00 M 1.93 0.00 1.54 3.20 0.00 2.81 0.00 0.00 0.19 1.10 0.00 0.00 0.22 1.61 0.00 1.41 0.00 0.00 0.00 0.00 M 0.66 0.38 1.57 2.78 0.00 1.15 0.00 0.41 0.00 1.67 0.00 1.50 0.00 0.81 0.00 0.22 0.00 1.13 0.85 0.87 M 0.81 0.00 0.85 0.00 0.35 3.99 1.36 1.91 0.00 0.23 0.00 0.00 0.00 0.00 0.00 0.68 0.00 1.25 0.00 2.57 M 1.62 0.00 0.00 0.00 0.00 7.74 0.79 1.52 0.00 0.82 0.00 0.00 0.00 0.82 0.00 0.68 0.00 0.00 0.00 0.00 M 2.63 0.00 0.40 3.63 0.00 0.65 0.00 0.00 0.00 1.50 0.00 0.00 0.00 2.07 0.00 1.17 0.42 1.52 0.00 0.00 M 3.00 0.51 1.37 4.05 0.68 0.00 0.00 0.00 0.00 0.68 0.00 0.00 0.00 0.74 0.82 0.19 1.11 0.00 0.00 0.85 M 3.59 0.00 0.00 0.00 0.68 0.00 0.00 0.21 0.85 4.81 0.00 0.00 0.00 0.00 0.00 0.81 0.40 1.15 0.00 1.50 M 1.17 0.00 0.00 0.00 0.82 2.84 0.00 0.81 0.00 5.35 0.00 0.85 0.00 0.00 0.00 0.40 1.07 0.00 0.00 0.68 M 0.00 0.00 0.21 2.52 0.81 0.28 0.00 2.04 0.82 0.00 0.00 0.00 0.00 0.99 3.51 0.93 0.68 0.00 0.35 0.85 M 0.00 0.00 0.00 0.85 0.81 0.25 0.00 0.68 0.00 3.99 0.00 0.00 0.00 0.82 4.88 0.22 0.00 1.50 0.00 0.00 M 0.00 0.00 0.00 0.00 0.40 0.00 0.00 1.19 2.48 5.77 2.99 0.00 0.00 0.00 0.00 0.00 0.34 0.00 0.00 0.82 M 0.00 0.00 0.00 0.68 4.61 0.82 0.00 0.96 0.00 1.42 0.00 0.85 0.82 0.00 0.00 0.00 0.00 3.02 0.00 0.81 M 0.21 0.00 0.82 0.82 0.17 0.85 0.35 1.10 1.83 1.66 0.00 0.00 0.00 1.11 0.00 0.42 0.21 4.44 0.00 0.00 M 0.89 0.00 0.00 0.00 0.00 0.85 0.00 0.00 0.68 0.00 0.00 0.77 0.00 0.00 0.00 3.26 2.32 1.76 0.00 3.47 M 1.49 0.00 0.85 0.00 1.06 0.00 1.58 0.00 0.00 0.00 0.00 0.00 4.66 0.82 0.00 0.00 0.00 0.82 0.00 2.72 M 0.68 0.00 0.00 0.00 0.00 0.82 0.00 0.85 0.00 0.00 0.00 0.82 6.03 0.00 0.00 0.00 0.00 0.00 3.99 0.81 M 0.68 0.00 0.00 1.36 0.00 0.00 0.82 0.82 0.00 0.85 0.00 0.00 1.00 1.96 0.00 1.13 5.38 0.00 0.00 0.00 M 0.68 0.00 0.00 0.00 0.82 0.81 0.00 0.00 0.68 0.82 0.00 0.00 0.00 3.47 0.51 0.00 5.35 0.85 0.00 0.00 M 0.00 0.00 0.81 0.00 0.00 0.68 0.00 0.00 5.51 1.36 0.00 0.00 0.82 0.00 3.99 0.00 0.00 0.00 0.00 0.82 M 2.24 0.00 0.51 0.85 3.25 0.00 0.00 0.00 0.82 1.49 0.00 0.00 0.00 0.28 0.00 0.00 3.25 0.00 0.00 1.31 M 0.81 0.00 0.00 0.00 6.33 0.00 0.00 0.00 1.36 0.00 0.68 0.00 0.00 0.00 0.00 0.00 0.00 0.82 0.00 3.99 M 0.19 0.00 1.26 0.76 7.67 0.00 0.51 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.00 1.94 0.85 0.00 0.00 0.00 M 0.17 0.00 1.88 0.00 1.49 0.85 0.47 0.00 0.82 0.00 0.00 0.82 3.25 0.00 0.00 3.86 0.40 0.00 0.00 0.00 M 0.82 0.00 0.00 0.00 4.66 0.00 4.80 0.00 2.19 0.68 0.00 0.00 0.00 0.00 0.00 0.00 0.85 0.00 0.00 0.00 M 0.00 0.00 0.82 0.00 4.61 3.99 0.00 0.00 1.49 0.68 0.00 0.00 0.85 0.00 0.00 0.82 0.00 0.00 0.74 0.00 M 1.59 0.00 6.62 0.00 0.81 0.00 0.00 0.00 2.04 0.82 0.00 1.29 0.82 0.00 0.00 0.00 0.00 0.00 0.00 0.00 M 0.85 0.00 0.68 0.00 0.00 0.82 1.11 0.00 0.00 7.06 0.00 0.25 0.00 0.00 0.00 1.55 1.50 0.17 0.00 0.00 M 0.68 0.00 0.00 0.82 0.00 0.00 0.96 0.82 0.00 1.36 0.00 0.21 0.00 1.06 0.00 7.34 0.00 0.74 0.00 0.00 M 2.27 0.00 0.00 0.42 0.00 0.68 1.48 0.00 1.36 0.82 0.00 0.57 0.99 1.17 0.00 3.31 0.11 0.81 0.00 0.00 [Part of this file has been deleted for brevity] T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 T 9.94 0.00 0.00 0.00 0.00 0.00 0.00 T 9.20 0.00 0.00 0.00 0.00 0.00 0.00 T 8.52 0.00 0.00 0.00 0.00 0.00 0.00 T 8.52 0.00 0.00 0.00 0.00 0.00 0.00 T 8.01 0.00 0.00 0.00 0.00 0.00 0.00 |
Program name | Description |
---|---|
ealistat | Statistics for multiple alignment files |
ehmmalign | Align sequences with an HMM |
ehmmcalibrate | Calibrate a hidden Markov model |
ehmmconvert | Convert between HMM formats |
ehmmemit | Extract HMM sequences |
ehmmfetch | Extract HMM from a database |
ehmmindex | Index an HMM database |
ehmmpfam | Align single sequence with an HMM |
ehmmsearch | Search sequence database with an HMM |
Although we take every care to ensure that the results of the EMBOSS version are identical to those from the original package, we recommend that you check your inputs give the same results in both versions before publication.
Please report all bugs in the EMBOSS version to the EMBOSS bug team, not to the original author.