
                                 ehmmalign 



Function

   Align sequences with an HMM

Description

   **************** EDIT HERE ****************

Algorithm

   **************** EDIT HERE ****************

Usage

   Here is a sample session with ehmmalign


% ehmmalign ../ehmmbuild-ex-keep/globin.hmm globins630.fa globins630.ali 
Align sequences with an HMM

Alignment saved in file globins630.ali

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-hmmfile]           infile     HMM file
  [-sequences]         seqset     Sequence set USA
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -mapalifile         infile     Map alignment
   -withalifile        infile     Heuristic alignment
   -matchonly          boolean    Only show match state alignment symbols

   Associated qualifiers:

   "-sequences" associated qualifiers
   -sbegin2            integer    Start of each sequence to be used
   -send2              integer    End of each sequence to be used
   -sreverse2          boolean    Reverse (if DNA)
   -sask2              boolean    Ask for begin/end/reverse
   -snucleotide2       boolean    Sequence is nucleotide
   -sprotein2          boolean    Sequence is protein
   -slower2            boolean    Make lower case
   -supper2            boolean    Make upper case
   -sformat2           string     Input sequence format
   -sdbname2           string     Database name
   -sid2               string     Entryname
   -ufo2               string     UFO features
   -fformat2           string     Features format
   -fopenfile2         string     Features file name

   "-outfile" associated qualifiers
   -odirectory3        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
   [-hmmfile]
   (Parameter 1) HMM file Input file Required
   [-sequences]
   (Parameter 2) Sequence set USA Readable set of sequences Required
   [-outfile]
   (Parameter 3) Output file name Output file <sequence>.ehmmalign
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   -mapalifile Map alignment Input file Required
   -withalifile Heuristic alignment Input file Required
   -matchonly Only show match state alignment symbols Boolean value
   Yes/No No

Input file format

   ehmmalign reads any normal sequence USAs.

  Input files for usage example

  File: ../ehmmbuild-ex-keep/globin.hmm

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 Jul 15 12:00:00 2005
CKSUM 5854
XT      -8455     -4      0      *  -8455     -4      0      *
NULT      -4  -8455
NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1
085   -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
//

  File: globins630.fa

> BAHG_VITSP
MLDQQTINIIKATVPVLKEHGVTITTTFYKNLFAKHPEVRPLFDMGRQESLEQPKALAM
TVLAAAQNIENLPAILPAVKKIAVKHCQAGVAAAHYPIVGQELLGAIKEVLGDAATDDIL
DAWGKAYGVIADVfiqveadLYAQAVE
> GLB1_ANABR
PSVQGAAAQLTADVKKDLRDSWKVIGSDKKGNGVALMTTLFADNQETIGYFKRLGNVSQ
GMANDKLRGHSITLMYALQNFIDQLDNTDDLVCVVEKFAVNHITRKISAAEFGKINGPIK
KVLASKNFGDKYANAWAKLVAVVQAAL
> GLB1_ARTSX
ERVDPITGLSGLEKNAILDTWGKVRGNLQEVGKATFGKLFAAHPEYQQMFRFFQGVQLA
FLVQSPKFAAHTQRVVSALDQTLLALNRPSDQFVYMIKELGLDHINRGTDRSFVEYLKES
LGDSVDEFTVQSFGEVIVNFLNEGLRQA
> GLB1_CALSO
VSANDIKNVQDTWGKLYDQWDAVHAsKFYNKLFKDSEDISEAFVKAGTGSGIAMKRQAL
VFGAILQEFVANLNDPTALTLKIKGLCATHKTRGITNMELFAFALADLVAYMGTtISFTA
AQKASWTAVNDVILHQMSSYFATVA
> GLB1_CHITH
GPSGDQIAAAKASWNTVKNNQVDILYAVFKANPDIQTAFSQFAGKDLDSIKGTPDFSKH
AGRVVGLFSEVMDLLGNDANTPTILAKAKDFGKSHKSRASPAQLDNFRKSLVVYLKGATK
WDSAVESSWAPVLDFVFSTLKNEL
> GLB1_GLYDI
GLSAAQRQVIAATWKDIAGADNGAGVGKDCLIKFLSAHPQMAAVFGFSGASDPGVAALG
AKVLAQIGVAVSHLGDEGKMVAQMKAVGVRHKGYGNKHIKAQYFEPLGASLLSAMEHRIG
GKMNAAAKDAWAAAYADISGALISGLQS
> GLB1_LUMTE
ECLVTEGLKVKLQWASAFGHAHQRVAFGLELwkgILREHPEIKAPFSRVRGDNIYSPQF
GAHSQRVLSGLDITISMLDTPDmLAAQLAHLKVQHVERNLKPEFFDIFLKHLLHVLGDRL
GTHFDFGAWHDCVDQIIDGIKDI
> GLB1_MORMR
PIVDSGSVSPLSDAEKNKIRAAWDLVYKDYEKTGVDILVKFFTGTPAAQAFFPKFKGLT
TADDLKQSSDVRWHAERIINAVNDAVKSMDDTEKMSMKLKELSIKHAQSFYVDRQYFKVL
AGIIADTTAPGDAGFEKLMSMICILLSSAY
> GLB1_PARCH
GGTLAIQSHGDLTLAQKKIVRKTWHQLMRNKTSFVTDLFIRIFAYDPAAQNKFPQMAGM
SASQLRSSRQMQAHAIRVSSIMSEYIEELDSDILPELLATLARTHDLNKVGPAHYDLFAK
VLMEALQAELGSDFNQKTRDSWAKAFSIVQAVLLVKHG
> GLB1_PETMA
PIVDSGSVPALTAAEKATIRTAWAPVYAKYQSTGVDILIKFFTSNPAAQAFFPKFQGLT
SADQLKKSMDVRWHAERIINAVNDAVVAMDDTEKMSLKLRELSGKHAKSFQVDPQYFKVL
AAVIVDTVLPGDAGLEKLMSMICILLRSSY
> GLB1_PHESE
DCNTLKRFKVKHQWQQVFSGEhHRTEFSLHFWKEFLHDHPDLVSLFKRVQGENIYSPEF
QAHGIRVLAGLDSVIGVLDEDDTFTVQLAHLKAQHTERGTKPEYFDLFGTQLFDILGDKL
GTHFDQAAWRDCYAVIAAGIKP
> GLB1_SCAIN
PSVYDAAAQLTADVKKDLRDSWKVIGSDKKGNGVALMTTLFADNQETIGYFKRLGNVSQ
GMANDKLRGHSITLMYALQNFIDQLDNPDDLVCVVEKFAVNHITRKISAAEFGKINGPIK
KVLASKNFGDKYANAWAKLVAVVQAAL
> GLB1_TYLHE
TDCGILQRIKVKQQWAQVYSVGESRTDFAIDVFNNFFRTNPDRSLFNRVNGDNVYSPEF


  [Part of this file has been deleted for brevity]

GLSDAEWQLVLNVWGKVEADLAGHGQEVLIRLFHTHPETLEKFDKFKHLKSEDEMKASE
DLKKHGNTVLTALGAILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISEAIIHVLHSKH
PGDFGADAQAAMSKALELFRNDIAAQYKELGFQG
> MYG_ROUAE
GLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE
DLKKHGATVLTALGGILKKKGQHEAQLKPLAQSHATKHKIPVKYLEFISEVIIQVLQSKH
PGDFGADAQGAMGKALELFRNDIAAKYKELGFQG
> MYG_SAISC
GLSDGEWQLVLNIWGKVEADIPSHGQEVLISLFKGHPETLEKFDKFKHLKSEDEMKASE
ELKKHGTTVLTALGGILKKKGQHEAELKPLAQSHATKHKIPVKYLELISDAIVHVLQKKH
PGDFGADAQGAMKKALELFRNDMAAKYKELGFQG
> MYG_SHEEP
GLSDGEWQLVLNAWGKVEADVAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASE
DLKKHGNTVLTALGGILKKKGHHEAEVKHLAESHANKHKIPVKYLEFISDAIIHVLHAKH
PSNFGADAQGAMSKALELFRNDMAAEYKVLGFQG
> MYG_SPAEH
GLSDGEWQLVLNVWGKVEGDLAGHGQEVLIKLFKNHPETLEKFDKFKHLKSEDEMKGSE
DLKKHGNTVLTALGGILKKKGQHAAEIQPLAQSHATKHKIPIKYLEFISEAIIQVLQSKH
PGDFGADAQGAMSKALELFRNDIAAKYKELGFQG
> MYG_TACAC
GLSDGEWQLVLKVWGKVETDITGHGQDVLIRLFKTHPETLEKFDKFKHLKTEDEMKASA
DLKKHGGVVLTALGSILKKKGQHEAELKPLAQSHATKHKISIKFLEFISEAIIHVLQSKH
SADFGADAQAAMGKALELFRNDMATKYKEFGFQG
> MYG_THUAL
ADFDAVLKCWGPVEADYTTMGGLVLTRLFKEHPETQKLFPKFAGIAQADIAGNAAISAH
GATVLKKLGELLKAKGSHAAILKPLANSHATKHKIPINNFKLISEVLVKVMHEKAGLDAG
GQTALRNVMGIIIADLEANYKELGFSG
> MYG_TUPGL
GLSDGEWQLVLNVWGKVEADVAGHGQEVLIRLFKGHPETLEKFDKFKHLKTEDEMKASE
DLKKHGNTVLSALGGILKKKGQHEAEIKPLAQSHATKHKIPVKYLEFISEAIIQVLQSKH
PGDFGADAQAAMSKALELFRNDIAAKYKELGFQG
> MYG_TURTR
GLSDGEWQLVLNVWGKVEADLAGHGQDVLIRLFKGHPETLEKFDKFKHLKTEADMKASE
DLKKHGNTVLTALGAILKKKGHHDAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRH
PAEFGADAQGAMNKALELFRKDIAAKYKELGFHG
> MYG_VARVA
GLSDEEWKKVVDIWGKVEPDLPSHGQEVIIRMFQNHPETQDRFAKFKNLKTLDEMKNSE
DLKKHGTTVLTALGRILKQKGHHEAEIAPLAQTHANTHKIPIKYLEFICEVIVGVIAEKH
SADFGADSQEAMRKALELFRNDMASRYKELGFQG
> MYG_VULCH
GLSDGEWQLVLNIWGKVETDLAGHGQEVLIRLFKNHPETLDKFDKFKHLKTEDEMKGSE
DLKKHGNTVLTALGGILKKKGHHEAELKPLAQSHATKHKIPVKYLEFISDAIIQVLQSKH
SGDFHADTEAAMKKALELFRNDIAAKYKELGFQG
> MYG_ZALCA
GLSDGEWQLVLNIWGKVEADLVGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKRSE
DLKKHGKTVLTALGGILKKKGHHDAELKPLAQSHATKHKIPIKYLEFISEAIIHVLQSKH
PGDFGADTHAAMKKALELFRNDIAAKYRELGFQG
> MYG_ZIPCA
GLSEAEWQLVLHVWAKVEADLSGHGQEILIRLFKGHPETLEKFDKFKHLKSEAEMKASE
DLKKHGHTVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSRH
PSDFGADAQAAMTKALELFRKDIAAKYKELGFHG

Output file format

   ehmmalign outputs a graph to the specified graphics device. outputs a
   report format file. The default format is ...

  Output files for usage example

  File: globins630.ali

#=AU HMMER 2.1.1
#=SQ BAHG_VITSP 1.0000 - - 0..0::0 -
#=SQ GLB1_ANABR 1.0000 - - 0..0::0 -
#=SQ GLB1_ARTSX 1.0000 - - 0..0::0 -
#=SQ GLB1_CALSO 1.0000 - - 0..0::0 -
#=SQ GLB1_CHITH 1.0000 - - 0..0::0 -
#=SQ GLB1_GLYDI 1.0000 - - 0..0::0 -
#=SQ GLB1_LUMTE 1.0000 - - 0..0::0 -
#=SQ GLB1_MORMR 1.0000 - - 0..0::0 -
#=SQ GLB1_PARCH 1.0000 - - 0..0::0 -
#=SQ GLB1_PETMA 1.0000 - - 0..0::0 -
#=SQ GLB1_PHESE 1.0000 - - 0..0::0 -
#=SQ GLB1_SCAIN 1.0000 - - 0..0::0 -
#=SQ GLB1_TYLHE 1.0000 - - 0..0::0 -
#=SQ GLB2_ANATR 1.0000 - - 0..0::0 -
#=SQ GLB2_CALSO 1.0000 - - 0..0::0 -
#=SQ GLB2_CHITH 1.0000 - - 0..0::0 -
#=SQ GLB2_LUMTE 1.0000 - - 0..0::0 -
#=SQ GLB2_MORMR 1.0000 - - 0..0::0 -
#=SQ GLB2_TYLHE 1.0000 - - 0..0::0 -
#=SQ GLB3_CHITH 1.0000 - - 0..0::0 -
#=SQ GLB3_CHITP 1.0000 - - 0..0::0 -
#=SQ GLB3_LAMSP 1.0000 - - 0..0::0 -
#=SQ GLB3_MORMR 1.0000 - - 0..0::0 -
#=SQ GLB3_MYXGL 1.0000 - - 0..0::0 -
#=SQ GLB3_PETMA 1.0000 - - 0..0::0 -
#=SQ GLB3_TYLHE 1.0000 - - 0..0::0 -
#=SQ GLB4_CHITH 1.0000 - - 0..0::0 -
#=SQ GLB4_GLYDI 1.0000 - - 0..0::0 -
#=SQ GLB4_LUMTE 1.0000 - - 0..0::0 -
#=SQ GLB4_TYLHE 1.0000 - - 0..0::0 -
#=SQ GLB5_PETMA 1.0000 - - 0..0::0 -
#=SQ GLB6_CHITH 1.0000 - - 0..0::0 -
#=SQ GLB7_ARTSX 1.0000 - - 0..0::0 -
#=SQ GLB7_CHITH 1.0000 - - 0..0::0 -
#=SQ GLB8_CHITH 1.0000 - - 0..0::0 -
#=SQ GLB9_CHITH 1.0000 - - 0..0::0 -
#=SQ GLBA_ANATR 1.0000 - - 0..0::0 -
#=SQ GLBA_SCAIN 1.0000 - - 0..0::0 -
#=SQ GLBB_ANATR 1.0000 - - 0..0::0 -
#=SQ GLBB_SCAIN 1.0000 - - 0..0::0 -
#=SQ GLBC_CAUAR 1.0000 - - 0..0::0 -
#=SQ GLBC_CHITH 1.0000 - - 0..0::0 -
#=SQ GLBD_CAUAR 1.0000 - - 0..0::0 -
#=SQ GLBD_CHITH 1.0000 - - 0..0::0 -
#=SQ GLBE_CHITH 1.0000 - - 0..0::0 -
#=SQ GLBF_CHITH 1.0000 - - 0..0::0 -
#=SQ GLBH_CHITH 1.0000 - - 0..0::0 -
#=SQ GLBI_CHITP 1.0000 - - 0..0::0 -
#=SQ GLBM_ANATR 1.0000 - - 0..0::0 -


  [Part of this file has been deleted for brevity]

MYG_GALJA   ...................
MYG_GLOME   ...................
MYG_GORBE   ...................
MYG_GRAGE   ...................
MYG_HALGR   ...................
MYG_HETPO   ...................
MYG_HORSE   ...................
MYG_HUMAN   ...................
MYG_HYLAG   ...................
MYG_INIGE   ...................
MYG_KOGSI   ...................
MYG_LAGLA   ...................
MYG_LAGMA   ...................
MYG_LEPMU   ...................
MYG_LOXAF   ...................
MYG_LUTLU   ...................
MYG_LYCPI   ...................
MYG_MACFA   ...................
MYG_MACRU   ...................
MYG_MEGNO   ...................
MYG_MELME   ...................
MYG_MESCA   ...................
MYG_MOUSE   ...................
MYG_MUSAN   ...................
MYG_NYCCO   ...................
MYG_OCHPR   ...................
MYG_ORCOR   ...................
MYG_ORNAN   ...................
MYG_ORYAF   ...................
MYG_PANTR   ...................
MYG_PAPAN   ...................
MYG_PERPO   ...................
MYG_PHOPH   ...................
MYG_PHYCA   ...................
MYG_PIG     ...................
MYG_PONPY   ...................
MYG_PROGU   ...................
MYG_RABIT   ...................
MYG_ROUAE   ...................
MYG_SAISC   ...................
MYG_SHEEP   ...................
MYG_SPAEH   ...................
MYG_TACAC   ...................
MYG_THUAL   ...................
MYG_TUPGL   ...................
MYG_TURTR   ...................
MYG_VARVA   ...................
MYG_VULCH   ...................
MYG_ZALCA   ...................
MYG_ZIPCA   ...................

Data files

   **************** EDIT HERE ****************

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name                Description
   ealistat      Statistics for multiple alignment files
   ehmmbuild     Build 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

Author(s)

   This program is an EMBOSS conversion of a program written by Sean Eddy
   as part of his HMMER package.

   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.

History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
