AB Generate HMM
Simple wrapper for hmmbuild from the HMMER3 package. The HMMER software must be installed on your system for this to work.
Currently there isn't a means to pass in hmmbuild-specific arguments. This could be implemented if you want it, just leave a note in the issue tracker.
Optional. If you have a weird alias for hmmbuild on your system, specify it.
11 6
Ate-PanxβD MASQIN
Ael-PanxβB M-VVIR
Ael-PanxβD M----E
Cla-PanxβD M--APP
Hec-PanxβD M-GSLG
Che-PanxβA MALVAS
Pph-PanxβD MSNIAG
Ccr-PanxγA M-----
Che-PanxβC M-AITD
Che-PanxβD M--APP
Ate-PanxβC MGFITG
4 17
Mle-Panxα9 -mldilskf- -kgvtpf
Mle-Panxα7 mgveilfpii nratapf
Mle-Panxα8 mvlevlalf- -prlapf
Mle-Panxα6 mlleilanf- -kgatpf
$: alb Panxs.phy -gh
# hmmbuild :: profile HMM construction from multiple sequence alignments
# HMMER 3.1b2 (February 2015); http://hmmer.org/
# Copyright (C) 2015 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# input alignment file: /Volumes/Zippy/.sysTemp/tmpdr0xnavx/align.sto
# output HMM file: /Volumes/Zippy/.sysTemp/tmpdr0xnavx/align.hmm
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# idx name nseq alen mlen eff_nseq re/pos description
#---- -------------------- ----- ----- ----- -------- ------ -----------
1 align 11 6 5 11.00 1.576
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
HMMER3/f [3.1b2 | February 2015]
NAME align
LENG 5
ALPH amino
RF no
MM no
CONS yes
CS no
MAP yes
DATE Tue Sep 26 15:09:42 2017
NSEQ 11
EFFN 11.000000
CKSUM 1016304395
STATS LOCAL MSV -5.4879 0.87586
STATS LOCAL VITERBI -6.0831 0.87586
STATS LOCAL FORWARD -2.0549 0.87586
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 2.40656 5.24437 3.64316 3.41685 3.65289 2.61149 4.82530 2.33280 3.89025 2.80187 1.59035 3.13843 2.94572 3.48436 3.58285 2.68302 2.97459 2.66811 5.76404 4.61514
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
0.00350 6.05380 6.77614 0.61958 0.77255 0.00000 *
1 6.27279 7.43337 7.13652 7.14713 6.43798 6.22710 7.57426 6.09490 7.11415 5.12953 0.02658 7.26617 6.86524 7.39204 6.99078 6.62335 6.72072 6.22382 7.85471 7.00088 1 M - - -
2.68328 4.42270 2.77565 2.73168 3.46399 2.40433 3.72540 3.29399 2.67786 2.69400 4.24735 2.90392 2.73785 3.18192 2.89846 2.37811 2.77565 2.98564 4.58522 3.61548
1.04041 0.88526 1.45207 0.02800 3.58939 0.48576 0.95510
2 2.21040 4.83844 4.65627 4.07780 2.23408 2.25900 4.70195 3.30262 3.97866 2.03076 3.96095 2.29162 4.76959 4.21871 4.20100 2.11716 3.55380 2.09677 5.45455 4.25637 3 l - - -
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
0.00488 5.72009 6.44244 0.61958 0.77255 0.49344 0.94294
3 1.93872 5.02585 5.11225 4.54418 4.19294 4.65341 5.05932 1.30264 4.41672 3.23682 4.18618 4.71264 5.05734 2.31154 4.58255 2.24773 3.80777 1.62434 5.72661 4.53566 4 i - - -
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
0.00412 5.88942 6.61177 0.61958 0.77255 1.01029 0.45274
4 1.65274 4.98203 5.35417 4.77508 4.12544 4.67065 5.10864 1.60577 4.60632 2.04239 4.12620 4.83131 2.10124 4.77816 4.68889 3.99795 1.74157 3.11875 5.67395 4.49503 5 i - - -
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
0.00412 5.88942 6.61177 0.61958 0.77255 0.25841 1.47963
5 3.57497 6.10792 2.43638 2.23794 5.44851 1.45209 4.51383 4.94232 3.28437 4.41215 5.15675 2.28350 2.21113 3.61814 2.44703 2.32076 3.81279 4.49753 6.53975 5.11283 6 g - - -
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
0.00252 5.98396 * 0.61958 0.77255 0.00000 *
//
# hmmbuild :: profile HMM construction from multiple sequence alignments
# HMMER 3.1b2 (February 2015); http://hmmer.org/
# Copyright (C) 2015 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# input alignment file: /Volumes/Zippy/.sysTemp/tmpdr0xnavx/align.sto
# output HMM file: /Volumes/Zippy/.sysTemp/tmpdr0xnavx/align.hmm
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# idx name nseq alen mlen eff_nseq re/pos description
#---- -------------------- ----- ----- ----- -------- ------ -----------
1 align 4 17 15 4.00 1.914
# CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
HMMER3/f [3.1b2 | February 2015]
NAME align
LENG 15
ALPH amino
RF no
MM no
CONS yes
CS no
MAP yes
DATE Tue Sep 26 15:09:42 2017
NSEQ 4
EFFN 4.000000
CKSUM 230807594
STATS LOCAL MSV -5.9125 0.74331
STATS LOCAL VITERBI -6.2029 0.74331
STATS LOCAL FORWARD -3.2946 0.74331
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 2.35458 5.26223 3.74639 2.95200 2.18960 3.12338 4.91982 2.55514 3.12047 1.95234 2.80918 3.94555 2.40578 4.32099 3.21362 3.42748 2.95799 2.58139 5.81769 4.53818
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
0.21344 5.15864 1.67958 0.61958 0.77255 0.00000 *
1 4.29858 5.71109 5.50293 5.30468 4.30282 4.86743 5.80310 3.63752 5.04075 2.83076 0.23849 5.42542 5.42188 5.37725 5.09102 4.69218 4.67584 3.75302 6.16430 5.01733 1 M - - -
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
0.01052 4.95572 5.67806 0.61958 0.77255 0.27371 1.42941
2 3.23323 4.63095 4.99515 4.41177 3.65356 1.68414 4.76966 2.75728 4.24454 1.70502 1.97117 4.50764 4.75380 4.41136 4.33208 3.71636 3.47467 1.65129 5.29712 4.13268 2 v - - -
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
0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510
3 4.20090 5.41098 6.18760 5.69269 3.93658 5.64129 6.16409 2.62596 5.56068 0.64879 3.68289 5.86391 5.76079 5.54287 5.56637 5.09235 4.44342 1.25015 6.18371 5.15682 3 L - - -
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
0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510
4 4.02473 6.82481 1.53890 0.52288 6.08247 4.01525 4.71665 5.71848 3.95544 5.13292 6.07920 3.46044 4.72969 3.91154 4.71508 3.82224 4.35549 5.21887 7.24565 5.60789 4 E - - -
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
0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510
5 3.99577 5.16207 6.16017 5.74849 4.61792 5.72078 6.70002 0.55009 5.73741 2.96197 4.30282 5.92187 5.91540 6.03582 5.94098 5.21149 4.26571 1.28588 6.90130 5.64974 5 I - - -
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
0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510
6 4.91943 6.07804 6.20575 5.96913 4.17473 5.59449 6.33051 3.51589 5.80807 0.14441 4.01175 6.19412 5.91567 5.82414 5.73219 5.58379 5.18804 3.83852 6.31563 5.30148 6 L - - -
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
0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510
7 1.10742 4.81268 4.69437 4.30994 1.44423 3.83993 4.97738 3.89753 4.25568 3.62108 4.53051 4.29474 4.54677 4.47434 4.46048 1.70427 3.47930 3.54208 5.83831 4.53125 7 a - - -
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
0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510
8 3.14293 5.38446 3.42688 2.91483 4.68347 3.89632 4.08626 4.10311 1.79783 2.00497 4.47847 2.09537 1.76591 3.22611 3.13676 3.15482 3.37273 3.76139 5.85564 4.53278 8 p - - -
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
0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510
9 4.28292 5.48494 6.02472 5.62953 0.76902 5.49017 5.19649 1.27918 5.47674 2.46876 3.91146 5.51961 5.69026 5.39403 5.43172 4.92522 4.52137 2.95762 5.28460 3.71682 9 f - - -
2.68645 4.42252 2.77547 2.73151 3.46381 2.40540 3.72522 3.29012 2.67768 2.69382 4.24717 2.90124 2.73767 3.18174 2.89828 2.37914 2.77547 2.98546 4.58504 3.61530
0.34615 1.23856 5.88099 0.68592 0.70042 0.48576 0.95510
10 3.93565 6.04374 4.49686 3.64453 5.66791 4.49118 4.28833 4.93499 1.07081 4.26073 5.13597 3.99189 1.87744 3.40896 1.26424 3.90194 4.05202 4.60760 6.21033 5.12224 12 k - - -
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
0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510
11 1.30908 5.10969 4.17204 3.76313 5.24195 1.21416 4.81082 4.67953 3.52007 4.28008 5.08365 4.01097 4.50906 4.01045 1.72645 3.24828 3.55407 4.11180 6.44140 5.22757 13 g - - -
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
0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510
12 1.94466 4.61596 4.86259 4.30271 3.80242 4.27754 4.76724 2.73646 4.16358 1.68774 3.76930 4.41649 4.69922 4.36625 4.29939 3.61247 1.57112 1.65574 5.38558 4.20158 14 t - - -
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
0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510
13 0.73090 4.91287 5.04065 4.88928 5.48025 3.73285 5.63589 4.78294 4.84392 4.59620 5.42446 4.51199 4.58116 5.02980 4.95249 3.22971 1.07959 4.10472 6.86118 5.77585 15 a - - -
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
0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510
14 5.05729 6.42579 5.73817 5.78480 6.50109 5.05594 6.59427 6.56747 5.97179 5.92399 7.10105 5.95881 0.05262 6.29187 5.94310 5.28930 5.57523 6.04327 7.18148 6.67383 16 P - - -
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
0.00858 5.15864 5.88099 0.61958 0.77255 0.48576 0.95510
15 5.28886 6.32458 6.04402 6.04967 0.12483 5.40825 5.07900 4.91272 5.99471 4.03003 5.48518 5.70494 5.91212 5.87824 5.82453 5.40816 5.62080 4.95635 5.17478 3.48272 17 F - - -
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
0.00578 5.15585 * 0.61958 0.77255 0.00000 *
//
Pass in the program name for hmmbuild if you have named it something other than hmmbuild. You can also specify a full path.
$: alb Panxs.stlkm -gh my_custom_hmmbuild
Assuming you have my_custom_hmmbuild in your $PATH,
you'll get the same output as in example 1.
