+++ /dev/null
-
-
-CLUSTAL-OMEGA is a general purpose multiple sequence alignment program
-for protein and DNA/RNA.
-
-
-
-INTRODUCTION
-
-Clustal-Omega is a general purpose multiple sequence alignment (MSA)
-program for protein and DNA/RNA. It produces high quality MSAs and is
-capable of handling data-sets of hundreds of thousands of sequences in
-reasonable time.
-
-In default mode, users give a file of sequences to be aligned and
-these are clustered to produce a guide tree and this is used to guide
-a "progressive alignment" of the sequences. There are also facilities
-for aligning existing alignments to each other, aligning a sequence to
-an alignment and for using a hidden Markov model (HMM) to help guide
-an alignment of new sequences that are homologous to the sequences
-used to make the HMM. This latter procedure is referred to as
-"external profile alignment" or EPA.
-
-Clustal-Omega uses HMMs for the alignment engine, based on the HHalign
-package from Johannes Soeding [1]. Guide trees are made using an
-enhanced version of mBed [2] which can cluster very large numbers of
-sequences in O(N*log(N)) time. Multiple alignment then proceeds by
-aligning larger and larger alignments using HHalign, following the
-clustering given by the guide tree.
-
-In its current form Clustal-Omega has been extensivly tested for
-protein sequences, DNA/RNA support has been added since version 1.1.0.
-
-
-
-SEQUENCE INPUT:
-
--i, --in, --infile={<file>,-}
- Multiple sequence input file (- for stdin)
-
---hmm-in=<file>
- HMM input files
-
---dealign
- Dealign input sequences
-
---profile1, --p1=<file>
- Pre-aligned multiple sequence file (aligned columns will be kept fixed)
-
---profile2, --p2=<file>
- Pre-aligned multiple sequence file (aligned columns will be kept fixed)
-
---is-profile
- disable check if profile, force profile (default no)
-
--t, --seqtype={Protein, RNA, DNA}
- Force a sequence type (default: auto)
-
---infmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]}
- Forced sequence input file format (default: auto)
-
-
-For sequence and profile input Clustal-Omega uses the Squid library
-from Sean Eddy [3].
-
-
-Clustal-Omega accepts 3 types of sequence input: (i) a sequence file
-with un-aligned or aligned sequences, (ii) profiles (a multiple
-alignment in a file) of aligned sequences, (iii) a HMM. Valid
-combinations of the above are:
-
-(a) one file with un-aligned or aligned sequences (i); the sequences
- will be aligned, and the alignment will be written out. For this
- mode use the -i flag. If the sequences are aligned (all sequences
- have the same length and at least one sequence has at least one
- gap), then the alignment is turned into a HMM, the sequences are
- de-aligned and the now un-aligned sequences are aligned using the
- HMM as an External Profile for External Profile Alignment (EPA).
- If no EPA is desired use the --dealign flag.
-
- Use the above option to make a multiple alignment from a set of
- sequences. A sequence file must contain more than one sequence (at
- least two sequences).
-
-(b) two profiles (ii)+(ii); the columns in each profile will be kept
- fixed and the alignment of the two profiles will be written
- out. Use the --p1 and --p2 flags for this mode.
-
- Use this option to align two alignments (profiles) together.
-
-
-(c) one file with un/aligned sequences (i) and one profile (ii); the
- profile is converted into a HMM and the un-aligned sequences will
- be multiply aligned (using the HMM background information) to form
- a profile; this constructed profile is aligned with the input
- profile; the columns in each profile (the original one and the one
- created from the un-aligned sequences) will be kept fixed and the
- alignment of the two profiles will be written out. Use the -i flag
- in conjunction with the --p1 flag for this mode.
- The un/aligned sequences file (i) must contain at least two
- sequences. If a single sequence has to be aligned with a profile
- the profile-profile option (b) has to be used.
-
- Use the above option to add new sequences to an existing
- alignment.
-
-(d) one file with un-aligned sequences (i) and one HMM (iii); the
- un-aligned sequences will be aligned to form a profile, using the
- HMM as an External Profile. So far only one HMM can be input and
- only HMMer2 and HMMer3 formats are allowed. The alignment will be
- written out; the HMM information is discarded. As, at the moment,
- only one HMM can be used, no HMM is produced if the sequences are
- already aligned. Use the -i flag in conjunction with the --hmm-in
- flag for this mode. Multiple HMMs can be inputted, however, in the
- current version all but the first HMM will be ignored.
-
- Use this option to make a new multiple alignment of sequences from
- the input file and use the HMM as a guide (EPA).
-
-Sequences that all have the same lengths but do not contain a single
-gap are by default not recognised as a profile. If these sequences are
-indeed a profile an not just a collection of unaligned sequences that
-happen to have the same length then specify the --is-profile flag.
-
-
-Invalid combinations of the above are:
-
-(v) an un/aligned sequence file containing just one sequence (i)
-
-(w) an un/aligned sequence file containing just one sequence and a profile
- (i)+(ii)
-
-(x) an un/aligned sequence file containing just one sequence and a HMM
- (i)+(iii)
-
-(y) two or more HMMs (iii)+(iii)+... cannot be aligned to one another.
-
-(z) one profile (ii) cannot be aligned with a HMM (iii)
-
-
-The following MSA file formats are allowed:
-
- a2m=fasta, (vienna)
- clustal,
- msf,
- phylip,
- selex,
- stockholm
-
-
-Prior to MSA, Clustal-Omega de-aligns all sequence input (i). However,
-alignment information is automatically converted into a HMM and used
-during MSA, unless the --dealign flag is specifically set. Profiles
-(ii) are not de-aligned.
-
-Since version 1.1.0 the Clustal-Omega alignment engine can process
-DNA/RNA. Clustal-Omega tries to guess the sequence type (protein,
-DNA/RNA), but this can be over-ruled with the --seqtype (-t) flag.
-
-
-CLUSTERING:
-
- --distmat-in=<file>
- Pairwise distance matrix input file (skips distance computation)
-
- --distmat-out=<file>
- Pairwise distance matrix output file
-
- --guidetree-in=<file>
- Guide tree input file
- (skips distance computation and guide tree clustering step)
-
- --guidetree-out=<file>
- Guide tree output file
-
- --full
- Use full distance matrix for guide-tree calculation (slow; mBed is default)
-
- --full-iter
- Use full distance matrix for guide-tree calculation during iteration (mBed is default)
-
- --cluster-size=<n>
- soft maximum of sequences in sub-clusters
-
- --clustering-out=<file>
- Clustering output file
-
- --use-kimura
- use Kimura distance correction for aligned sequences (default no)
-
- --percent-id
- convert distances into percent identities (default no)
-
-In order to produce a multiple alignment Clustal-Omega requires a
-guide tree which defines the order in which sequences/profiles are
-aligned. A guide tree in turn is constructed, based on a distance
-matrix. Conventionally, this distance matrix is comprised of all the
-pair-wise distances of the sequences. The distance measure
-Clustal-Omega uses for pair-wise distances of un-aligned sequences is
-the k-tuple measure [4], which was also implemented in Clustal 1.83
-and ClustalW2 [5,6]. If the protein sequences inputted via -i are
-aligned, then Clustal-Omega uses pairwise aligned identities, these
-distances can be Kimura-corrected [7] by specifying --use-kimura. The
-distances between aligned DNA/RNA sequences are determined from the
-alignment, no Kimura correction can be used. The computational effort
-(time/memory) to calculate and store a full distance matrix grows
-quadratically with the number of sequences. Clustal-Omega can improve
-this scalability to N*log(N) by employing a fast clustering algorithm
-called mBed [2]; this option is automatically invoked (default). If a
-full distance matrix evaluation is desired, then the --full flag has
-to be set. The mBed mode calculates a reduced set of pair-wise
-distances. These distances are used in a k-means algorithm, that
-clusters at most 100 sequences. For each cluster a full distance
-matrix is calculated. No full distance matrix (of all input sequences)
-is calculated in mBed mode. If there are less than 100 sequences in
-the input, then in effect a full distance matrix is calculated in mBed
-mode, however, no distance matrix can be outputted (see below).
-
-
-Clustal-Omega uses Muscle's [8] fast UPGMA implementation to construct
-its guide trees from the distance matrix. By default, the distance
-matrix is used internally to construct the guide tree and is then
-discarded. By specifying --distmat-out the internal distance matrix
-can be written to file. This is only possible in --full or --full-iter
-mode. The guide trees by default are used internally to guide the
-multiple alignment and are then discarded. By specifying the
---guidetree-out option these internal guide trees can be written out
-to file. Conversely, the distance calculation and/or guide tree
-building stage can be skipped, by reading in a pre-calculated distance
-matrix and/or pre-calculated guide tree. These options are invoked by
-specifying the --distmat-in and/or --guidetree-in flags,
-respectively. However, distance matrix reading is disabled in the
-current version. By default, distance matrix and guide tree files are
-not over-written, if a file with the specified name already exists. In
-this case Clustal-Omega aborts during the command-line processing
-stage. To force over-writing of already existing files use the --force
-flag (see MISCELLANEOUS). In mBed mode a full distance matrix cannot
-be outputted, distance matrix output is only possible in --full mode.
-mBed or --full distance mode do not affect the ability to write out
-guide-trees. It is possible to perform an initial mBed (not-full)
-distance calculation and a subsequent full distance calculation (see
-section ITERATION). In this case a distance matrix can be outputted.
-
-Guide trees can be iterated to refine the alignment (see section
-ITERATION). Clustal-Omega takes the alignment, that was produced
-initially and constructs a new distance matrix from this alignment.
-The distance measure used at this stage is a full alignment distance
-(as opposed the initial pairwise k-tuple distance); distances of
-protein sequences can be Kimura corrected [7], DNA/RNA distances are
-not. By default, Clustal-Omega constructs a reduced distance matrix at
-this stage using the mBed algorithm, which will then be used to create
-an improved (iterated) new guide tree. To turn off mBed-like
-clustering at this stage the --full-iter flag has to be set. While
-full alignment distances in general are much faster to calculate than
-k-tuple distances, time and memory requirements still scale
-quadratically with the number of sequences and --full-iter clustering
-should only be considered for smaller cases (<< 10,000 sequences) or
-if response time and resources are not an issue.
-
-The default cluster size in mBed mode is 100. This means that
-sequences are grouped into clusters with a soft maximum of 100
-sequences, full distance matrices are calculated for these clusters,
-guide-trees are calculated for the clusters and the clusters are then
-strung together with an over-arching guide-tree. It is possible to
-change the cluster-size with the --cluster-size flag. The clustering
-can be outputted to file. The output is comprised of the cluster
-index, a running index for the sequences within each cluster, the
-running index for the sequence within the input file, the name of the
-sequence and the bi-section sequence (see EXAMPLES).
-
-Clustal-Omega uses pair-distances. Between unaligned sequences these
-are so called k-tuple distance, between aligned sequences they are
-full alignment distances, as employed by Squid. These values range
-between 0.0 (identical) and 1.0 (completely different). The distances
-are used to construct the guide-tree and are by default outputted if
---distmat-out is specified (and --full and/or --full-iter are
-set). For full alignment distances there is a so called Kimura
-correction [7] which more closely reflects evolutionary
-distance. Kimura-corrected distances range from 0.0 (identical) to
-theoretically infinity (completely different). In practice there
-appears to be a maximum value. In Clustal-Omega these Kimura-corrected
-distance can be outputted for protein if the --use-kimura flag is
-specified. Kimura correction is not available for DNA/RNA. Up to and
-including version 1.1.1 Kimura-corrected distances were outputted by
-default (where possible). Since version 1.2.0 the default is to output
-uncorrected distances.
-
-
-Pair-distances closely correspond to percentage pair-wise identities
-through i=100*(1-d), where i is the percentage pair-wise identity and
-d is the pair-wise distance. Percentage pair-wise identities can be
-outputted in Clustal-Omega instead of the distance matrix by
-specifying the --percent-id flag as well as --distmat-out, --full
-and/or --full-iter. Percentage pair-wise identities cannot be
-outputted if --use-kimura is specified.
-
-
-ALIGNMENT OUTPUT:
-
- -o, --out, --outfile={file,-}
- Multiple sequence alignment output file (default: stdout)
-
- --outfmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]}
- MSA output file format (default: fasta)
-
- --residuenumber, --resno
- in Clustal format print residue numbers (default no)
-
- --wrap=<n>
- number of residues before line-wrap in output
-
- --output-order={input-order,tree-order}
- MSA output order like in input/guide-tree
-
-
-By default Clustal-Omega writes its results (alignments) to stdout. An
-output file can be specified with the -o flag. Output to stdout is not
-possible in verbose mode (-v, see MISCELLANEOUS) as verbose/debugging
-messages would interfere with the alignment output. By default,
-alignment files are not over-written, if a file with the specified
-name already exists. In this case Clustal-Omega aborts during the
-command-line processing stage. To force over-writing of already
-existing files use the --force flag (see MISCELLANEOUS).
-
-Clustal-Omega can output alignments in various formats by setting the
---outfmt flag:
-
- * for Fasta format set: --outfmt=a2m or --outfmt=fa or --outfmt=fasta
-
- * for Clustal format set: --outfmt=clu or --outfmt=clustal
-
- * for Msf format: set --outfmt= msf
-
- * for Phylip format set: --outfmt=phy or --outfmt=phylip
-
- * for Selex format set: --outfmt=selex
-
- * for Stockholm format set: --outfmt=st or --outfmt=stockholm
-
- * for Vienna format set: --outfmt=vie or --outfmt=vienna
-
-In ClustalW one could print the residue number of the last residue in
-each line in Clustal-Format. This feature can be turned on by setting
-the --resno or --residuenumber flag.
-
-The line lengths in Clustal Format is usually 60 residues, in Fasta
-format it is usually 60 or 80 residues. This value can be set using
-the --wrap flag.
-
-By default the order of sequences in the output is the same as in the
-input (--output-order=input-order). This can be changed to the order
-in which the sequences appear in the guide-tree by setting
---output-order=tree-order.
-
-
-ITERATION:
-
- --iterations, --iter=<n> Number of (combined guide tree/HMM) iterations
-
- --max-guidetree-iterations=<n> Maximum guide tree iterations
-
- --max-hmm-iterations=<n> Maximum number of HMM iterations
-
-
-By default, Clustal-Omega calculates (or reads in) a guide tree and
-performs a multiple alignment in the order specified by this guide
-tree. This alignment is then outputted. Clustal-Omega can 'iterate'
-its guide tree. The hope is that the full alignment distances, that
-can be derived from the initial alignment, will give rise to a better
-guide tree, and by extension, to a better alignment.
-
-A similar rationale applies to HMM-iteration. MSAs in general are very
-'vulnerable' at their early stages. Sequences that are aligned at an
-early stage remain fixed for the rest of the MSA. Another way of
-putting this is: 'once a gap, always a gap'. This behaviour can be
-mitigated by HMM iteration. An initial alignment is created and turned
-into a HMM. This HMM can help in a new round of MSA to 'anticipate'
-where residues should align. This is using the HMM as an External
-Profile and carrying out iterative EPA. In practice, individual
-sequences and profiles are aligned to the External HMM, derived after
-the initial alignment. Pseudo-count information is then transferred to
-the (internal) HMM, corresponding to the individual
-sequence/profile. The now somewhat 'softened' sequences/profiles are
-then in turn aligned in the order specified by the guide
-tree. Pseudo-count transfer is reduced with the size of the
-profile. Individual sequences attain the greatest pseudo-count
-transfer, larger profiles less so. Pseudo-count transfer to profiles
-larger than, say, 10 is negligible. The effect of HMM iteration is
-more pronounced in larger test sets (that is, with more sequences).
-
-Both, HMM- and guide tree-iteration come at a cost of increasing the
-run-time. One round of guide tree iteration adds on (roughly) the time
-it took to construct the initial alignment. If, for example, the
-initial alignment took 1min, then it will take (roughly) 2min to
-iterate the guide tree once, 3min to iterate the guide tree twice, and
-so on. HMM-iteration is more costly, as each round of iteration adds
-three times the time required for the alignment stage. For example, if
-the initial alignment took 1min, then each additional round of HMM
-iteration will add on 3min; so 4 iterations will take 13min
-(=1min+4*3min). The factor of 3 stems from the fact that at every
-stage both intermediate profiles have to be aligned with the
-background HMM, and finally the (softened) HMMs have to be aligned as
-well. All times are quoted for single processors.
-
-By default, guide tree iteration and HMM-iteration are coupled. This
-means, at each iteration step both, guide tree and HMM, are
-re-calculated. This is invoked by setting the --iter flag. For
-example, if --iter=1, then first an initial alignment is produced
-(without external HMM background information and using k-tuple
-distances to calculate the guide tree). This initial alignment is then
-used to re-calculate a new guide tree (using full alignment distances)
-and to create a HMM. The new guide tree and the HMM are then used to
-produce a new MSA.
-
-Iteration of guide tree and HMM can be de-coupled. This means that the
-number of guide tree iterations and HMM iterations can be
-different. This can be done by combining the --iter flag with the
---max-guidetree-iterations and/or the --max-hmm-iterations flag. The
-number of guide tree iterations is the minimum of --iter and
---max-guidetree-iterations, while the number of HMM iterations is the
-minimum of --iter and --max-hmm-iterations. If, for example, HMM
-iteration should be performed 5 times but guide tree iteration should
-be performed only 3 times, then one should set --iter=5 and
---max-guidetree-iterations=3. All three flags can be specified at the
-same time (however, this makes no sense). It is not sufficient just to
-specify --max-guidetree-iterations and --max-hmm-iterations but not
---iter. If any iteration is desired, then --iter has to be
-set. Conversely, if no alignment is desired but only distance
-calculation and tree construction, then --max-hmm-iterations=-1 will
-terminate the calculation before the alignment stage; --iter does not
-have to be specified in this case.
-
-
-LIMITS (will exit early, if exceeded):
-
- --maxnumseq=<n> Maximum allowed number of sequences
-
- --maxseqlen=<l> Maximum allowed sequence length
-
-Limits can be imposed on the number of sequences in the input file
-and/or the lengths of the sequences. This cap can be set with the
---maxnumseq and --maxseqlen flags, respectively. Clustal-Omega will
-exit early, if these limits are exceeded.
-
-
-MISCELLANEOUS:
-
- --auto Set options automatically (might overwrite some of your options)
-
- --threads=<n> Number of processors to use
-
- -l, --log=<file> Log all non-essential output to this file
-
- -h, --help Print help and exit
-
- -v, --verbose Verbose output (increases if given multiple times)
-
- --version Print version information and exit
-
- --long-version Print long version information and exit
-
- --force Force file overwriting
-
-
-Users may feel unsure which options are appropriate in certain
-situations even though using ClustalO without any special options
-should give you the desired results. The --auto flag tries to
-alleviate this problem and selects accuracy/speed flags according to
-the number of sequences. For all cases will use mBed and thereby
-possibly overwrite the --full option. For more than 1,000 sequences
-the iteration is turned off as the effect of iteration is more
-noticeable for 'larger' problems. Otherwise iterations are set to 1 if
-not already set to a higher value by the user. Expert users may want
-to avoid this flag and exercise more fine tuned control by selecting
-the appropriate options manually.
-
-Certain parts of the MSA calculation have been parallelised. Most
-noticeably, the distance matrix calculation, and certain aspects of
-the HMM building stage. Clustal-Omega uses OpenMP. By default,
-Clustal-Omega will attempt to use as many threads as possible. For
-example, on a 4-core machine Clustal-Omega will attempt to use 4
-threads. The number of threads can be limited by setting the --threads
-flag. This may be desirable, for example, in the case of
-benchmarking/timing.
-
-Usually, non-essential (verbose) output is written to screen. This
-output can be written to file by specifying the --log flag.
-
-Help is available by specifying the -h flag.
-
-By default Clustal-Omega does not print any information to stdout
-(other than the final alignment, if no output file is
-specified). Information concerning the progress of the alignment can
-be obtained by specifying one verbosity flag (-v). This may be
-desirable, to verify what Clustal-Omega is actually doing at the
-moment. If two verbosity flags (-v -v) are specified, command-line
-flags (explicitly and implicitly set) are printed in addition to the
-progress report. Triple verbose level (-v -v -v) is the most verbose
-level. In addition to single- and double-verbose information much more
-information is displayed: input sequences and names, details of the
-tree construction and intermediate alignments. Tree construction
-information includes pairwise distances. The number of pairwise
-distances scales with the square of the number of sequences, and
-double verbose mode is probably only useful for a small number of
-sequences.
-
-The current version number of Clustal-Omega can be displayed by
-setting the --version flag.
-
-The current version number of Clustal-Omega as well as the code-name
-and the build date can be displayed by setting the --long-version
-flag.
-
-By default, Clustal-Omega does not over-write files. These can be (i)
-alignment output, (ii) distance matrix and (iii) guide
-tree. Overwriting can be forced by setting the --force flag.
-
-
-EXAMPLES:
-
-./clustalo -i globin.fa
-
-Clustal-Omega reads the sequence file globin.fa, aligns the sequences
-and prints the result to screen in fasta/a2m format.
-
-
-./clustalo -i globin.fa -o globin.sto --outfmt=st
-
-If the file globin.sto does not exist, then Clustal-Omega reads the
-sequence file globin.fa, aligns the sequences and prints the result to
-globin.sto in Stockholm format. If the file globin.sto does exist
-already, then Clustal-Omega terminates the alignment process before
-reading globin.fa.
-
-
-./clustalo -i globin.fa -o globin.aln --outfmt=clu --force
-
-Clustal-Omega reads the sequence file globin.fa, aligns the sequences
-and prints the result to globin.aln in Clustal format, overwriting the
-file globin.aln, if it already exists.
-
-
-./clustalo -i globin.fa --distmat-out=globin.mat --guidetree-out=globin.dnd --force
-
-Clustal-Omega reads the sequence file globin.fa, aligns the sequences,
-prints the result to screen in fasta/a2m format (default), the guide
-tree to globin.dnd and the distance matrix to globin.mat, overwriting
-those files if they already exist.
-
-
-./clustalo -i globin.fa --guidetree-in=globin.dnd
-
-Clustal-Omega reads the files globin.fa and globin.dnd, skipping
-distance calculation and guide tree creation, using instead the guide
-tree specified in globin.dnd.
-
-
-./clustalo -i globin.fa --hmm-in=PF00042.hmm
-
-Clustal-Omega reads the sequence file globin.fa and the HMM file
-PF00042.hmm (in HMMer2 or HMMer3 format). It then performs the
-alignment, transferring pseudo-count information contained in
-PF00042.hmm to the sequences/profiles during the MSA.
-
-
-./clustalo -i globin.sto
-
-Clustal-Omega reads the file globin.sto (of aligned sequences in
-Stockholm format). It converts the alignment into a HMM, de-aligns the
-sequences and re-aligns them, transferring pseudo-count information to
-the sequences/profiles during the MSA. The guide tree is constructed
-using a full distance matrix.
-
-
-./clustalo -i globin.sto --dealign
-
-Clustal-Omega reads the file globin.sto (of aligned sequences in
-Stockholm format). It de-aligns the sequences and then re-aligns
-them. No HMM is produced in the process, no pseudo-count information
-is transferred. Consequently, the output must be the same as for
-unaligned output (like in the first example ./clustalo -i globin.fa)
-
-
-./clustalo -i globin.fa --iter=2
-
-Clustal-Omega reads the file globin.fa, creates a UPGMA guide tree
-built from k-tuple distances, and performs an initial alignment. This
-initial alignment is converted into a HMM and a new guide tree is
-built from the (preliminary) full alignment distances of the initial
-alignment. The un-aligned sequences are then aligned (for the second
-time but this time) using pseudo-count information from the HMM
-created after the initial alignment (and using the new guide
-tree). This second alignment is then again converted into a HMM and a
-new guide tree is constructed. The un-aligned sequences are then
-aligned (for a third time), again using pseudo-count information of
-the HMM from the previous step and the most recent guide tree. The
-final alignment is written to screen.
-
-
-./clustalo -i globin.fa --iter=5 --max-guidetree-iterations=1
-
-Clustal-Omega reads the file globin.fa, creates a UPGMA guide tree
-built from k-tuple distances, and performs an initial alignment. This
-initial alignment is converted into a HMM and a new guide tree is
-built from the (preliminary) full alignment distances of the initial
-alignment. The un-aligned sequences are then aligned (for the second
-time but this time) using pseudo-count information from the HMM
-created after the initial alignment (and using the new guide
-tree). For the last 4 iterations the guide tree is left unchanged and
-only HMM iteration is performed. This means that intermediate
-alignments are converted to HMMs, and these intermediate HMMs are used
-to guide the MSA during subsequent iteration stages.
-
-
-./clustalo -i globin.fa -o globin.a2m -v
-
-In case the file globin.a2m does not exist, Clustal-Omega reads the
-file globin.fa, prints a progress report to screen and writes the
-alignment in (default) Fasta format to globin.a2m. The progress report
-consists of the number of threads used, the number of sequences read,
-the current progress in the k-tuple distance calculation, completion
-of the guide tree computation and current progress of the MSA stage.
-If the file globin.a2m already exists Clustal-Omega aborts before
-reading the file globin.fa. Note that in verbose mode an output file
-has to be specified, because progress/debugging information, which is
-printed to screen, would interfere with the alignment being printed to
-screen.
-
-
-./clustalo -i PF00042_full.fa --dealign --full --outfmt=vie -o PF00042_full.vie --force
-
-Clustal-Omega reads the file PF00042_full.fa. This file contains
-several thousand aligned sequences. --dealign tells Clustal-Omega to
-erase all alignment information and re-align the sequences from
-scratch. As there are several thousand sequences calculating a full
-distance matrix may be slow. Setting the --full flag specifically
-selects the full distance mode over the default mBed mode. The
-alignment is then written out in Vienna format (fasta format all on
-one line, no line breaks per sequence) to file PF00042_full.vie.
-
-
-./clustalo -i PF00042_full.fa --dealign --outfmt=vie -o PF00042_full.vie --force
-
-Clustal-Omega reads the file PF00042_full.fa. This file contains
-several thousand aligned sequences. --dealign tells Clustal-Omega to
-erase all alignment information and re-align the sequences from
-scratch. Calculating the distance matrix will be done by mBed
-(default). Clustal-Omega will calculate pairwise distances to a
-small number of reference sequences only. This will give a significant
-speed-up. The speed-up is greater for larger families (more
-sequences). The alignment is then written out in Vienna format (fasta
-format all on one line, no line breaks per sequence) to file
-PF00042_full.vie.
-
-
-./clustalo --p1=globin.sto --p2=PF00042_full.vie -o globin+pf00042.fa
-
-Clustal-Omega reads files globin.sto and PF00042_full.vie of aligned
-sequences (profiles). Both profiles are then aligned. The relative
-positions of residues in both profiles are not changed during this
-alignment, however, columns of gaps may be inserted into the profiles,
-respectively. The final alignment is written to file globin+pf00042.fa
-in fasta format.
-
-
-./clustalo -i globin.fa --p1=PF00042_full.vie -o pf00042+globin.fa
-
-Clustal-Omega reads file globin.fa of un-aligned sequences and the
-profile (of aligned sequences) in file PF00042_full.vie. A HMM is
-created from the profile. This HMM is used to guide the alignment of
-the un-aligned sequences in globin.fa. The profile that was generated
-during this alignment of un-aligned globin.fa sequences is then
-aligned to the input profile PF00042_full.vie. The relative positions
-of residues in profile PF00042_full.vie is not changed during this
-alignment, however, columns of gaps may be inserted into the
-profile. The final alignment is output to file pf00042+globin.fa in
-fasta format. The alignment in this example may be slightly different
-from the alignment in the previous example, because no HMM guidance
-was used generate the profile globin.sto. In this example HMM guidance
-was used to align the sequences in globin.fa; the hope being that this
-intermediate alignment will have profited from the bigger profile.
-
-
-./clustalo -i globin.fa --clustering-out=globin.aux --cluster-size=3
-
-globin.fa contains 7 sequences. Usually a full distance matrix is
-created for less than 100 sequences. This is over-written by
-specifying --cluster-size=3. Clustal-Omega attempts to create clusters
-of no more than 3 sequences. This clustering is recorded in the file
-globin.aux which looks like
-
- Cluster 0: object 0 has index 0 (=seq P1|HBB_HUMAN ) 00
- Cluster 0: object 1 has index 1 (=seq P1|HBB_HORSE ) 00
- Cluster 1: object 0 has index 4 (=seq P1|MYG_PHYCA ) 1
- Cluster 1: object 1 has index 5 (=seq P1|GLB5_PETMA ) 1
- Cluster 1: object 2 has index 6 (=seq P1|LGB2_LUPLU ) 1
- Cluster 2: object 0 has index 2 (=seq P1|HBA_HUMAN ) 01
- Cluster 2: object 1 has index 3 (=seq P1|HBA_HORSE ) 01
-
-There are 3 clusters, named Cluster~0, Cluster~1 and
-Cluster~2. Cluster~0 has 2 sequences, which are sequence 0 and 1 from
-the input file, named P1|HBB_HUMAN and P1|HBB_HORSE. Cluster~1 has 3
-sequences, sequences 4,5,6 from the input file and Cluster~2 has 2
-sequences, sequences 2 and 3 from the input file. The binary string at
-the end of each line encode the bi-section that led to this
-clustering. The first digit indicated the initial split. The '0'
-indicates that in the first split sequences 0,1,2,3 were grouped
-together and the '1' that sequences 4,5,6 were grouped together. The
-size of Cluster~1 does not exceed --cluster-size, so it does need to
-be broken up. The Cluster (with the initial '0') containing sequences
-0,1,2,3 is comprised of 4 sequences; this number exceed
---cluster-size, so that it will have to be broken up. This second
-split is indicated by the second digit of the binary string. The
-second '0' indicates that sequences 0,1 fall into one Cluster (which
-will ultimately be Cluster~0), and the second '1' indicates that
-sequences 2,3 fall into another cluster (ultimately Cluster~2).
-
-
-LITERATURE:
-
-[1] Johannes Soding (2005) Protein homology detection by HMM-HMM
- comparison. Bioinformatics 21 (7): 951–960.
-
-[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.
-
git://source.jalview.org / jabaws.git / blobdiff