eomegash |
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Clustal-Omega (clustalo) is a general purpose multiple sequence alignment (MSA) program for proteins. It produces high quality MSAs and is capable of handling data-sets of hundreds of thousands of sequences in reasonable time.
In its current form Clustal-Omega can only align protein sequences but not DNA/RNA sequences. It is envisioned that DNA/RNA will become available in a future version.
% eomegash ../data/globins4.hmm Sequence with HMM (ClustalO wrapper) (aligned) output sequence set [twoglob.aln]: WARNING: This is a beta version of Clustal Omega, for protein only. |
Go to the input files for this example
Go to the output files for this example
Sequence with HMM (ClustalO wrapper) Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequences] seqset File containing sequences to align [-hmm] infile Pre-aligned multiple sequence file (aligned columns will be kept fixed) [-outseq] seqoutset [ |
Qualifier | Type | Description | Allowed values | Default |
---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||
[-sequences] (Parameter 1) |
seqset | File containing sequences to align | Readable set of sequences | Required |
[-hmm] (Parameter 2) |
infile | Pre-aligned multiple sequence file (aligned columns will be kept fixed) | Input file | Required |
[-outseq] (Parameter 3) |
seqoutset | Sequence set filename and optional format (output USA) | Writeable sequences | <*>.format |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-indist | infile | Pairwise distance matrix input file (skips distance computation) | Input file | Required |
-inguide | infile | Guide tree input file (skips distance computation and guide tree clustering step) | Input file | Required |
-dealign | toggle | Dealign input sequences | Toggle value Yes/No | No |
-mbed | toggle | Fast, Mbed-like clustering for guide tree calculation | Toggle value Yes/No | No |
-intermbed | toggle | Fast, Mbed-like clustering for guide tree calculation | Toggle value Yes/No | No |
-maxiterations | integer | Number of (combined guide tree/HMM) iterations | Integer from 0 to 2000000000 | 0 |
-maxgiterations | integer | Maximum guide tree iterations | Integer from 0 to 2000000000 | 2000000000 |
-maxhiterations | integer | Maximum number of HMM iterations | Integer from 0 to 2000000000 | 2000000000 |
-maxseqs | integer | Maximum number of sequences | Integer from 2 to 2000000000 | 2000000000 |
-maxlenseq | integer | Maximum length of sequence | Integer from 1 to 2000000000 | 2000000000 |
-self | toggle | Set options automatically (might overwrite some options | Toggle value Yes/No | No |
-outdist | outfile | Pairwise distance matrix output file | Output file | <*>.eomegash |
-outguide | outfile | Guide tree output file | Output file | <*>.eomegash |
Associated qualifiers | ||||
"-sequences" associated seqset qualifiers | ||||
-sbegin1 -sbegin_sequences |
integer | Start of each sequence to be used | Any integer value | 0 |
-send1 -send_sequences |
integer | End of each sequence to be used | Any integer value | 0 |
-sreverse1 -sreverse_sequences |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
-sask1 -sask_sequences |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
-snucleotide1 -snucleotide_sequences |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
-sprotein1 -sprotein_sequences |
boolean | Sequence is protein | Boolean value Yes/No | N |
-slower1 -slower_sequences |
boolean | Make lower case | Boolean value Yes/No | N |
-supper1 -supper_sequences |
boolean | Make upper case | Boolean value Yes/No | N |
-sformat1 -sformat_sequences |
string | Input sequence format | Any string | |
-sdbname1 -sdbname_sequences |
string | Database name | Any string | |
-sid1 -sid_sequences |
string | Entryname | Any string | |
-ufo1 -ufo_sequences |
string | UFO features | Any string | |
-fformat1 -fformat_sequences |
string | Features format | Any string | |
-fopenfile1 -fopenfile_sequences |
string | Features file name | Any string | |
"-outseq" associated seqoutset qualifiers | ||||
-osformat3 -osformat_outseq |
string | Output seq format | Any string | |
-osextension3 -osextension_outseq |
string | File name extension | Any string | |
-osname3 -osname_outseq |
string | Base file name | Any string | |
-osdirectory3 -osdirectory_outseq |
string | Output directory | Any string | |
-osdbname3 -osdbname_outseq |
string | Database name to add | Any string | |
-ossingle3 -ossingle_outseq |
boolean | Separate file for each entry | Boolean value Yes/No | N |
-oufo3 -oufo_outseq |
string | UFO features | Any string | |
-offormat3 -offormat_outseq |
string | Features format | Any string | |
-ofname3 -ofname_outseq |
string | Features file name | Any string | |
-ofdirectory3 -ofdirectory_outseq |
string | Output directory | Any string | |
"-outdist" associated outfile qualifiers | ||||
-odirectory | string | Output directory | Any string | |
"-outguide" associated outfile qualifiers | ||||
-odirectory | string | Output directory | Any string | |
General qualifiers | ||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N |
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
-warning | boolean | Report warnings | Boolean value Yes/No | Y |
-error | boolean | Report errors | Boolean value Yes/No | Y |
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
-die | boolean | Report dying program messages | Boolean value Yes/No | Y |
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
>HBA_HUMAN P69905 Hemoglobin subunit alpha (Alpha-globin) (Hemoglobin alpha chain) MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP AVHASLDKFLASVSTVLTSKYR >HBA_BOVFRAG Hemoglobin subunit alpha (Alpha-globin) fragment (Hemoglobin alpha chain) DKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG AKVAAALTKAVEHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTP AVHASLDKFLANVST |
HMMER3/b [3.0 | March 2010] NAME globins4 LENG 149 ALPH amino RF no CS no MAP yes DATE Fri Jul 15 12:00:00 2011 NSEQ 4 EFFN 0.964844 CKSUM 2027839109 STATS LOCAL MSV -9.9014 0.70957 STATS LOCAL VITERBI -10.7224 0.70957 STATS LOCAL FORWARD -4.1637 0.70957 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 COMPO 2.36553 4.52577 2.96709 2.70473 3.20818 3.02239 3.41069 2.90041 2.55332 2.35210 3.67329 3.19812 3.45595 3.16091 3.07934 2.66722 2.85475 2.56965 4.55393 3.62921 2.68640 4.42247 2.77497 2.73145 3.46376 2.40504 3.72516 3.29302 2.67763 2.69377 4.24712 2.90369 2.73719 3.18168 2.89823 2.37879 2.77497 2.98431 4.58499 3.61525 0.57544 1.78073 1.31293 1.75577 0.18968 0.00000 * 1 1.70038 4.17733 3.76164 3.36686 3.72281 3.29583 4.27570 2.40482 3.29230 2.54324 3.63799 3.55099 3.93183 3.61602 3.56580 2.71897 2.84104 1.67328 5.32720 4.10031 9 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.03156 3.86736 4.58970 0.61958 0.77255 0.34406 1.23405 2 2.62748 4.47174 3.31917 2.82619 3.63815 3.49607 2.75382 3.03401 2.75280 2.74783 3.65114 3.24714 2.62341 3.12082 3.11124 2.79244 2.89355 1.88003 5.06315 3.77128 10 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 3 3.50771 4.88753 4.66754 4.31907 3.27776 4.35743 4.88268 2.50779 4.08449 0.57907 3.22569 4.56607 4.74802 4.37991 4.20749 3.97946 3.79191 2.62059 5.25407 4.04279 11 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 4 2.34080 4.28719 3.51550 3.22063 4.37406 3.06195 4.29366 3.74891 3.24370 3.47337 4.31943 3.39310 3.80273 3.56072 3.55390 1.08280 2.00280 3.23325 5.72380 4.49519 12 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 5 2.04218 4.87966 2.77126 1.92448 4.32563 3.33660 3.78415 3.73388 2.61886 3.34029 4.16568 2.96714 2.18012 2.94561 3.07633 2.70238 2.96803 3.36068 5.56791 4.21854 13 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 6 1.67844 4.79514 2.78469 2.00544 4.34945 2.26719 3.85010 3.76260 2.72087 3.37961 4.20641 2.99947 3.85561 3.02442 3.17766 2.68798 2.96575 3.36703 5.60901 4.27005 14 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 7 3.05756 5.63998 1.78612 1.06702 4.93093 3.31407 3.86695 4.45859 2.89031 3.95237 4.80915 2.77798 3.94091 3.03432 3.48933 2.93505 3.34810 4.02575 6.09427 4.58708 15 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 8 2.98085 4.92154 3.50401 2.91209 3.76425 3.70161 3.75301 3.57060 1.24921 3.12012 4.04714 3.32210 4.09411 3.00014 2.54951 3.05147 3.18982 3.31354 2.52964 3.70813 16 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 9 2.59353 4.69451 3.03503 2.60972 4.18917 3.33498 3.80536 3.60013 2.58953 3.21847 4.04944 3.07115 3.85428 2.20828 2.99231 2.14672 1.84753 3.23346 5.45458 4.14691 17 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 10 2.23880 4.76665 3.06952 2.55248 4.02235 3.47005 3.69787 3.40277 2.01551 2.36330 3.87991 2.51243 3.88223 2.86967 2.84293 2.72413 2.90300 3.10205 5.29826 3.99496 18 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 11 3.19694 4.48391 4.99800 4.51340 3.70437 4.59686 5.22508 1.39091 4.40799 2.19554 3.49619 4.71017 4.90059 4.67186 4.59646 3.99910 3.46528 0.94853 5.69937 4.48740 19 - - [Part of this file has been deleted for brevity] 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 134 2.87148 5.44150 1.98118 1.74899 4.74617 3.33260 3.73791 4.25433 2.62738 3.72942 4.52187 2.07888 3.87291 2.23146 3.17389 2.78299 3.13122 3.81624 5.87307 4.40314 150 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 135 3.27331 5.22456 3.46754 3.04631 4.68046 3.71770 3.96365 4.13172 0.69147 3.63653 4.59195 3.45354 4.20521 3.14539 2.53832 3.30173 3.50915 3.82642 5.61930 4.48069 151 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 136 2.13728 4.25596 4.26822 3.70038 2.51560 3.93283 4.27242 2.28282 3.58922 1.68324 3.19522 3.92448 4.28790 3.80594 3.78003 3.23864 3.04401 1.82614 4.90639 3.70545 152 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 137 3.25266 4.59255 4.86528 4.29758 3.18898 4.50160 4.83534 2.17302 4.15958 1.11276 2.09173 4.53148 4.72252 4.28685 4.28308 3.84128 3.47963 1.79006 5.20435 4.12672 153 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 138 1.79466 4.79782 2.82404 1.94090 4.31166 3.30608 3.81075 3.72422 2.65702 3.33717 4.15830 2.99339 3.84716 2.97720 3.11199 2.03142 2.93949 3.33667 5.56525 4.22435 154 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 139 2.58506 4.29342 3.55405 3.00981 3.47023 2.68992 3.90060 2.80129 2.93915 2.04902 2.51305 3.37662 3.96778 3.25166 3.26632 2.35763 2.84501 2.57968 4.93542 3.70537 155 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 140 3.08583 4.40689 4.84510 4.29544 2.25790 4.37874 4.73777 1.57472 4.17210 1.94826 3.22641 4.44953 4.66205 4.33233 4.29141 3.72292 3.32617 1.35939 5.16135 3.94030 156 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 141 2.02979 2.61338 3.45168 2.91840 3.84883 3.32836 3.92100 3.21873 2.81248 2.91084 3.77423 3.27409 3.86642 3.17756 2.28029 2.17107 2.82032 2.90332 5.22633 3.98297 157 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 142 2.65037 4.69800 3.11777 2.58559 3.93396 3.48363 3.71066 2.49275 2.05906 2.95516 3.80693 2.50024 3.88815 2.89605 2.88872 2.72907 2.42763 2.99850 5.24239 3.94877 158 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 143 2.21701 4.52657 2.45380 2.75014 3.73535 3.53805 3.84294 2.86807 2.75770 2.17002 3.64455 3.21159 3.95457 3.08148 3.16791 2.80094 2.89608 2.24528 5.16549 3.89225 159 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 144 3.41438 4.70993 5.04893 4.51836 3.21871 4.71073 5.05993 1.60681 4.34794 0.90468 3.01922 4.76098 4.89446 4.48359 4.45935 4.09339 3.64659 2.14279 5.32906 4.22624 160 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 145 1.66341 4.55765 3.29747 2.78822 4.09563 3.34088 3.86205 3.44543 2.60980 3.11452 3.96692 3.19039 3.87148 3.05878 2.16675 2.67137 2.29043 3.09965 5.38848 4.12438 161 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 146 1.96741 4.60402 3.09101 2.67267 4.09875 3.30287 2.64764 3.55483 2.68845 3.18630 4.02165 3.11035 3.84730 3.04694 3.09548 1.72418 2.88008 3.18467 5.41006 4.09565 162 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 147 2.02427 4.88556 3.14956 2.70898 4.40362 3.45865 3.80224 3.73109 1.30907 3.34916 4.21424 3.15279 3.95761 2.96243 2.65527 2.83485 3.06573 3.38348 5.54009 4.27566 163 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510 148 3.70647 5.07328 4.29292 4.08736 2.37118 4.18885 3.80078 3.67800 3.93734 3.05218 4.32316 4.11065 4.65987 4.16910 4.05541 3.80923 3.99693 3.56378 4.02310 0.58497 164 - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 0.19360 4.17053 1.82902 0.61958 0.77255 0.48576 0.95510 149 2.92198 5.11574 3.28049 2.65489 4.47826 3.59727 2.51142 3.88373 1.57593 3.35205 4.19259 3.10178 3.96579 2.72398 1.84611 2.91372 3.10363 3.55066 5.42147 4.18835 165 - - 2.68634 4.42241 2.77536 2.73098 3.46370 2.40469 3.72511 3.29370 2.67757 2.69331 4.24706 2.90363 2.73756 3.18097 2.89817 2.37903 2.77536 2.98535 4.58493 3.61418 0.22163 1.61553 * 1.50361 0.25145 0.00000 * // |
>HBA_HUMAN P69905 Hemoglobin subunit alpha (Alpha-globin) (Hemoglobin alpha chain) MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP AVHASLDKFLASVSTVLTSKYR >HBA_BOVFRAG Hemoglobin subunit alpha (Alpha-globin) fragment (Hemoglobin alpha chain) ------DKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG AKVAAALTKAVEHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTP AVHASLDKFLANVST------- |
[2] Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence embedding for fast construction of guide trees for multiple sequence alignment. Algorithms Mol Biol. 2010 May 14;5:21.
[3] http://www.genetics.wustl.edu/eddy/software/#squid
[4] Wilbur and Lipman, 1983; PMID 6572363
[5] Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
[6] Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
[7] Kimura M (1980). "A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences". Journal of Molecular Evolution 16: 111–120.
[8] Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.
Program name | Description |
---|---|
edialign | Local multiple alignment of sequences |
emma | Multiple sequence alignment (ClustalW wrapper) |
eomega | Multiple sequence alignment (ClustalO wrapper) |
eomegapp | Profile with profile (ClustalO wrapper) |
eomegasp | Sequence with profile (ClustalO wrapper) |
infoalign | Display basic information about a multiple sequence alignment |
mse | Multiple Sequence Editor |
plotcon | Plot conservation of a sequence alignment |
prettyplot | Draw a sequence alignment with pretty formatting |
showalign | Display a multiple sequence alignment in pretty format |
tranalign | Generate an alignment of nucleic coding regions from aligned proteins |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.