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clustalO-profile.yaml
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clustalO-profile.yaml
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!mobyle/program
name: clustalO-profile
title: 'Clustal-Omega: Profile alignment'
description: Align 2 profiles (alignments)
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparagraph
comment: "the columns in each profile will be kept\n fixed and the alignment\
\ of the two profiles will be written\n out.Use this option to align\
\ two alignments (profiles) together."
prompt: Data Input
name: input
children:
- !mobyle/inputprogramparameter
prompt: Pre-aligned multiple sequence file (aligned columns will be kept
fixed)
format: '" --profile1=" + str( value )'
simple: true
mandatory: true
name: profile1
command: false
type: !mobyle/formattedtype
format_terms: ['EDAM_format:2200', 'EDAM_format:1982', 'EDAM_format:1961',
'EDAM_format:1993']
data_terms: ['EDAM_data:1384']
- !mobyle/inputprogramparameter
prompt: Pre-aligned multiple sequence file (aligned columns will be kept
fixed)
format: '" --profile2=" + str( value )'
simple: true
mandatory: true
name: profile2
command: false
type: !mobyle/formattedtype
format_terms: ['EDAM_format:2200', 'EDAM_format:1982', 'EDAM_format:1961',
'EDAM_format:1993']
data_terms: ['EDAM_data:1384']
- !mobyle/inputprogramparagraph
comment: "In order to produce a multiple alignment Clustal-Omega requires\
\ a\n guide tree which defines the order in which sequences/profiles\
\ are\n aligned. A guide tree in turn is constructed, based on\
\ a distance\n matrix. Conventionally, this distance matrix is\
\ comprised of all the\n pair-wise distances of the sequences.\
\ The distance measure\n Clustal-Omega uses for pair-wise distances\
\ of un-aligned sequences is\n the k-tuple measure [4], which\
\ was also implemented in Clustal 1.83\n and ClustalW2\n \
\ [5,6]. If the sequences inputted via -i are aligned\n \
\ Clustal-Omega uses the Kimura-corrected pairwise aligned identities\n\
\ [7]. The computational effort (time/memory) to calculate and\
\ store a\n full distance matrix grows quadratically with the\
\ number of sequences.\n Clustal-Omega can improve this scalability\
\ to N*log(N) by employing a\n fast clustering algorithm called\
\ mBed [2]; this option is\n automatically invoked (default).\
\ If a full distance matrix evaluation\n is desired, then the\
\ --full flag has to\n be set. The mBed mode\n calculates\
\ a reduced set of pair-wise distances. These distances are\n \
\ used in a k-means algorithm, that clusters at most 100 sequences. For\n\
\ each cluster a full distance matrix is calculated. No full\
\ distance\n matrix (of all input sequences) is calculated in\
\ mBed mode. If there\n are less than 100 sequences in the input,\
\ then in effect a full\n distance matrix is calculated in mBed\
\ mode, however, no distance\n matrix can be outputted (see below).Clustal-Omega\
\ uses Muscle's [8] fast UPGMA implementation to construct\n \
\ its guide trees from the distance matrix. By default, the distance\n\
\ matrix is used internally to construct the guide tree and is\
\ then\n discarded. By specifying --distmat-out the internal\
\ distance matrix\n can be written to file. This is only possible\
\ in --full mode. The\n guide trees by default are used internally\
\ to guide the multiple\n alignment and are then discarded. By\
\ specifying the --guidetree-out\n option these\n internal\
\ guide trees can be written out to\n file. Conversely, the distance\
\ calculation and/or guide tree building\n stage can be skipped,\
\ by reading in a pre-calculated distance matrix\n and/or pre-calculated\
\ guide tree. These options are invoked by\n specifying the --distmat-in\
\ and/or --guidetree-in flags,\n respectively. However, distance\
\ matrix reading is disabled in the\n current version. By default,\
\ distance matrix and guide tree files are\n not over-written,\
\ if a file with the specified name already\n exists. In\n \
\ this case Clustal-Omega aborts during the command-line processing\n\
\ stage. In mBed mode a full distance matrix cannot\n \
\ be outputted, distance matrix output is only possible in --full mode.\n\
\ mBed or --full distance mode do not affect the ability to write\
\ out\n guide-trees.Guide trees can be iterated to refine the\
\ alignment (see section\n ITERATION). Clustal-Omega takes the\
\ alignment, that was produced\n initially and constructs a new\
\ distance matrix from this alignment.\n The distance measure\
\ used at this stage is the Kimura distance [7]. By\n default,\
\ Clustal-Omega constructs a reduced distance matrix at this\n \
\ stage using the mBed algorithm, which will then be used to create\
\ an\n improved (iterated) new guide tree. To turn off mBed-like\
\ clustering\n at this\n stage the --full-iter flag\
\ has to be set. While Kimura\n distances in general are much\
\ faster to calculate than k-tuple\n distances, time and memory\
\ requirements still scale quadratically with\n the number of\
\ sequences and --full-iter clustering should only be\n considered\
\ for smaller cases ( << 10,000 sequences).[2] Blackshields G, Sievers\
\ F, Shi W, Wilm A, Higgins DG. Sequence\n embedding for fast\
\ construction of guide trees for multiple\n sequence alignment.\
\ Algorithms Mol Biol. 2010 May 14;5:21.[4] Wilbur and Lipman, 1983; PMID\
\ 6572363[5] Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving\n\
\ the sensitivity of progressive multiple sequence alignment\
\ through\n sequence weighting, position-specific gap penalties\
\ and weight\n matrix choice. Nucleic Acids Res., 22, 4673-4680.[6]\
\ Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA,\n \
\ McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson\
\ JD,\n Gibson TJ, Higgins DG. (2007). Clustal W and Clustal\
\ X version\n 2.0. Bioinformatics, 23, 2947-2948.[7] Kimura M\
\ (1980). \"A simple method for estimating evolutionary\n rates\
\ of base substitutions through comparative studies of\n nucleotide\
\ sequences\". Journal of Molecular Evolution 16: 111\u2013120."
prompt: Clustering
name: clustering
children:
- !mobyle/inputprogramparameter
prompt: Guide tree input file (--guidetree-in)
format: ( "" , " --guidetree-in="+str(value))[ value is not None ]
name: guidetree_in
command: false
type: !mobyle/formattedtype
format_terms: ['EDAM_format:1910']
data_terms: ['EDAM_data:0872']
- !mobyle/inputprogramparameter
prompt: Use full distance matrix for guide-tree calculation (slow; mBed
is default) (--full)
format: ( "" , " --full ")[ value is not None and value ]
name: full
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Use full distance matrix for guide-tree calculation during iteration
(mBed is default) (--full-iter)
format: ( "" , " --full-iter ")[ value is not None and value ]
name: full_iter
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparagraph
prompt: Alignment Output
name: output_format
children:
- !mobyle/inputprogramparameter
prompt: alignment output format
format: ( "" , " --outfmt=" + value )[ value is not None and value !=
vdef ]
name: output_format
command: false
type: !mobyle/stringtype
default: fasta
options:
- {label: fasta, value: fasta}
- {label: clustal, value: clustal}
- {label: msf, value: msf}
- {label: phylip, value: phylip}
- {label: stockholm, value: stockholm}
- {label: vienna, value: vienna}
- !mobyle/inputprogramparagraph
comment: "By default, Clustal-Omega calculates (or reads in) a guide tree\
\ and\n performs a multiple alignment in the order specified\
\ by this guide\n tree. This alignment is then outputted. Clustal-Omega\
\ can 'iterate'\n its guide tree. The hope is that the (Kimura)\
\ distances, that can be\n derived from the initial alignment,\
\ will give rise to a better guide\n tree, and by extension,\
\ to a better alignment.A similar rationale applies to HMM-iteration.\
\ MSAs in general are very\n 'vulnerable' at their early stages.\
\ Sequences that are aligned at an\n early stage remain fixed\
\ for the rest of the MSA. Another way of\n putting this is:\
\ 'once a gap, always a gap'. This behaviour can be\n mitigated\
\ by HMM iteration. An initial alignment is created and turned\n \
\ into a HMM. This HMM can help in a new round of MSA to 'anticipate'\n\
\ where residues should align. This is using the HMM as an External\n\
\ Profile and carrying out iterative EPA. In practice, individual\n\
\ sequences and profiles are aligned to the External HMM, derived\
\ after\n the initial alignment. Pseudo-count information is\
\ then transferred to\n the (internal) HMM, corresponding to\
\ the individual\n sequence/profile. The now somewhat 'softened'\
\ sequences/profiles are\n then in turn aligned in the order\
\ specified by the guide\n tree. Pseudo-count transfer is reduced\
\ with the size of the\n profile. Individual sequences attain\
\ the greatest\n pseudo-count\n transfer, larger profiles\
\ less so. Pseudo-count transfer to profiles\n larger than, say,\
\ 10 is negligible. The effect of HMM iteration is\n more pronounced\
\ in larger test sets (that is, with more sequences).Both, HMM- and guide\
\ tree-iteration come at a cost of increasing the\n run-time.\
\ One round of guide tree iteration adds on (roughly) the time\n \
\ it took to construct the initial alignment. If, for example, the\n\
\ initial alignment took 1min, then it will take (roughly) 2min\
\ to\n iterate the guide tree once, 3min to iterate the guide\
\ tree twice, and\n so on. HMM-iteration is more costly, as each\
\ round of iteration adds\n three times the time required for\
\ the alignment stage. For example, if\n the initial alignment\
\ took 1min, then each additional round of HMM\n iteration will\
\ add on 3min; so 4 iterations will take 13min\n (=1min+4*3min).\
\ The factor of 3 stems from the fact that at every\n stage both\
\ intermediate profiles have to be aligned with the\n background\
\ HMM, and finally the (softened) HMMs have to be aligned as\n \
\ well. All times are quoted for single processors.By default, guide\
\ tree iteration and HMM-iteration are coupled. This\n means,\
\ at each iteration step both, guide tree and HMM, are\n re-calculated.\
\ This is invoked by setting the --iter flag. For\n example,\
\ if --iter=1, then first an initial alignment is produced\n \
\ (without external HMM background information and using k-tuple\n \
\ distances to calculate the guide tree). This initial alignment\
\ is then\n used to re-calculate a new guide tree (using Kimura\
\ distances) and to\n create a HMM. The new\n guide\
\ tree and the HMM are then used to produce\n a new MSA.Iteration\
\ of guide tree and HMM can be de-coupled. This means that the\n \
\ number of guide tree iterations and HMM iterations can be\n \
\ different. This can be done by combining the --iter flag with the\n\
\ --max-guidetree-iterations and/or the --max-hmm-iterations\
\ flag. The\n number of guide tree iterations is the minimum\
\ of --iter and\n --max-guidetree-iterations, while the number\
\ of HMM iterations is the\n minimum of --iter and --max-hmm-iterations.\
\ If, for example, HMM\n iteration should be\n performed\
\ 5 times but guide tree iteration should\n be performed only\
\ 3 times, then one should set --iter=5 and\n --max-guidetree-iterations=3.\
\ All three flags can be specified at the\n same time (however,\
\ this makes no sense). It is not sufficient just to\n specify\
\ --max-guidetree-iterations and --max-hmm-iterations but not\n \
\ --iter. If any iteration is desired --iter has to be set."
prompt: Iteration
name: iteration
children:
- !mobyle/inputprogramparameter
prompt: Number of (combined guide-tree/HMM) iterations (--iter)
format: ( "" , " --iter="+str(value) )[ value is not None ]
name: iterations
command: false
type: !mobyle/integertype {}
- !mobyle/inputprogramparameter
prompt: Maximum number guidetree iterations (--max-guidetree-iterations)
format: ( "" , " --max-guidetree-iterations="+str(value) )[ value is not
None ]
name: max_guidetree_iterations
command: false
type: !mobyle/integertype {}
- !mobyle/inputprogramparameter
prompt: Maximum number of HMM iterations (--max-hmm-iterations)
format: ( "" , " --max-hmm-iterations="+str(value) )[ value is not None
]
name: max_hmm_iterations
command: false
type: !mobyle/integertype {}
- !mobyle/inputprogramparagraph
prompt: Miscellaneous
name: miscellaneous
children:
- !mobyle/inputprogramparameter
comment: "Users may feel unsure which options are appropriate in certain\n\
\ situations even though using ClustalO without any special\
\ options\n should give you the desired results. The\
\ --auto flag tries to\n alleviate this problem and selects\
\ accuracy/speed flags according to\n the number of sequences.\
\ For all cases will use mBed and thereby\n possibly\
\ overwrite the --full option. For more than 1,000 sequences\n \
\ the iteration is turned off as the effect of iteration\
\ is more\n noticeable for 'larger'\n problems.\
\ Otherwise iterations are set to 1 if\n not already\
\ set to a higher value by the user. Expert users may want\n \
\ to avoid this flag and exercise more fine tuned control\
\ by selecting\n the appropriate options manually."
prompt: Set options automatically (might overwrite some of your options)
(--auto)
format: ( "" , " --auto ")[value is not None and value]
name: auto
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
format: '" -v --force --log=clustalO_log"'
argpos: 100
name: verbosity
command: false
hidden: true
type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparameter
prompt: Multiple Sequence Alignment
filenames: '"clustalO-profile.out"'
name: alignment_output
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:1384']
- !mobyle/outputprogramparameter
prompt: Clustal omega log file
filenames: '"clustalO_log"'
name: logfile
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"clustalO-profile.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
comment: "Use this interface to align two alignments (profiles) together.The columns\
\ in each profile will be kept\n fixed and the alignment of the two profiles\
\ will be written\n out."
operations: ['EDAM_operation:0512']
topics: ['EDAM_topic:0080', 'EDAM_topic:0182']
command: clustalo
env: {}