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Topic: Clustal

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	ClustalW
		Clustal W is a major update and rewrite of the Clustal V program which was described in:
		The usage of Clustal W is largely the same as for Clustal V details of which are described in clustalv.doc.
		In Clustal V we used a simple formula to convert an observed distance to one that is corrected for multiple hits.
	www.u.arizona.edu /~schluter/ClustalW/ClustalW.html (3286 words)

	[No title]
		CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice.
		In the original CLUSTAL programs (17-19), the initial guide trees, used to guide the multiple alignment, were calculated using the UPGMA method (20).
		In CLUSTAL W, before any pair of sequences or prealigned groups of sequences are aligned, we generate a table of gap opening penalties for every position in the two (sets of) sequences.
	www.csc.fi /molbio/progs/clustalw/ms.html (4554 words)

	North Carolina Bioportal : Documentation (Site not responding. Last check: 2007-10-21)
		Evolutionary relationships derived by Clustal W can be visualized using Cladograms or Phylograms, which are “tree-like” representations of the sequence alignments.
		Clustal W combines a hierarchical method for multiple sequence alignment with a simple interface.
		Clustal W can read a secondary structure ‘mask’ and bias the position of the gaps according to it.
	www.ncbiogrid.org /training/mod2/clustal.html (544 words)

	Optimization case study: Clustal (Site not responding. Last check: 2007-10-21)
		Clustal is a tool used in computational biology (bioinformatics) to perform "multiple alignments".
		The first thing we want to know is whether clustal itself is the cause of its slowness, or if it's spending time in libraries or other programs.
		We note that clustal prints out a lot of diagnostic information while it's running, so our next step is to modify the expect script to disable logging to stdout.
	h21007.www2.hp.com /dspp/files/unprotected/linux/Optimization_case_study_Clustal.htm (3016 words)

	Help for secondary structure / gap penalty masks (Site not responding. Last check: 2007-10-21)
		Therefore CLUSTAL W now allows gap penalty masks to be supplied with the input sequences.
		In CLUSTAL format, capital residues denote the A and B core structure notation.
		In CLUSTAL format, loops are specified by "." in the secondary structure notation.
	www.sacs.ucsf.edu /Documentation/seqsoftware/ClustalW1.7/helpB.html (514 words)

	Using PILEUP (Site not responding. Last check: 2007-10-21)
		CLUSTAL is another multiple alignment program which is available on the RCR's Alpha server.
		CLUSTAL is also available as a stand-alone program for Macintosh and Windows computers.
		CLUSTAL also has a function to compute phylogenetic trees from a set of aligned sequences.
	www.med.nyu.edu /rcr/rcr/course/malign-clustal.html (322 words)

	[No title]
		README for Clustal W version 1.7 June 1997 Clustal W version 1.7 Documentation This file provides some notes on the latest changes, installation and usage of the Clustal W multiple sequence alignment program.
		With CLUSTAL format, this is just the same as the output format of this program and Clustal V. If you use PILEUP or CLUSTAL format, all sequences must be the same length, INCLUDING GAPS ("-" in clustal format; "." in MSF).
		Terminal Gaps In the original Clustal V program, terminal gaps were penalised the same as all other gaps.
	www.umanitoba.ca /afs/plant_science/psgendb/build/framework.old/doc/clustalw/clustalw.doc (3052 words)

	clustal.html (Site not responding. Last check: 2007-10-21)
		Higgins, D.G. and Sharp, P.M. Clustal: a package for performing multiple sequence alignment on a microcomputer.
		This old version (in Fortran) is accessible in SQX environment by keying "clustal".
		CLUSTAL is a program for performing multiple alignments of up to 100 DNA or protein sequences of up to 5000 residues (including gaps in the final alignment).
	www.infobiogen.fr /doc/SQXdoc/clustal.html (2019 words)

	Clustal - Wikipedia, the free encyclopedia
		Clustal is a widely used multiple sequence alignment computer program.
		Included NBRF/PIR, Fasta, EMBL/Swissprot, Clustal, GCC/MSF, GCG9 RSF and GDE.
		Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T.J., Higgins, D.G. and Thompson, J.D. (2003) Multiple sequence alignment with the Clustal series of programs.
	en.wikipedia.org /wiki/Clustal (327 words)

	Clustalw - BioPerl
		Previous versions were called ClustalV [4] which itself was an upgrade of the Clustal package [5].
		The ClustalW multiple alignment format is a human and computer readable format that represents the alignment in ASCII text.
		Higgins DG, Bleasby AJ, and Fuchs R. CLUSTAL V: improved software for multiple sequence alignment.
	www.bioperl.org /wiki/Clustalw (235 words)

	[No title]
		Phylogenetic trees S. Execute a system command H. EXIT (leave program) Your choice: Clustal W is a general purpose multiple alignment program for DNA or proteins.
		CLUSTAL format is recognised by the word CLUSTAL at the beginning of the file.
		Press [RETURN] to continue or X to stop: The paper describing Clustal W is: Thompson, J.D., Higgins, D.G. and Gibson, T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice.
	uts.cc.utexas.edu /~deanhend/blindcat/data/dna/paco/paco/Pl-1.12snew.out.txt (1708 words)

	Current Protocols in Bioinfomatics
		The Clustal programs are widely used for carrying out automatic multiple alignment of sets of nucleotide or amino acid sequences.
		Nonetheless, Clustal also has extensive facilities for adding sequences to existing alignments, merging existing alignments (so-called profile alignment as described in the Alternate Protocol), realignment of sections of alignment, detecting and fixing alignment errors, and basic phylogenetic analysis.
		The first Clustal programs were run on PCs only and were written as a series of stand-alone Fortran programs (Clustal1-4) that were run one after another in order to produce the multiple alignment (Higgins and Sharp, 1988, 1989).
	www.does.org /cp/bioinprotocol.html (6726 words)

	[No title] (Site not responding. Last check: 2007-10-21)
		Clustal X is a free alignment program, that can be downloaded from various sites in the internet.
		As Clustal X itself can import many file formats, it would be possible to save a file in the FASTA or NEXUS format, load it into Clustal X, export the data to NEXUS, and read it again with QuickAlign.
		The first time Clustal X is needed, you will be asked to locate it.
	www.uni-bonn.de /~uzsfjj/HTML/clustal.htm (354 words)

	CLUSTALW On-Line Help
		Clustal W is a general purpose multiple alignment program for DNA or proteins.
		The CLUSTAL is the matrix used by BESTFIT for comparison of nucleic acid sequences.
		Hydrophilic gap penalties are used to increase the chances of a gap within a run (5 or more residues) of hydrophilic amino acids; these are likely to be loop or random coil regions where gaps are more common.
	bioinformatics.utmem.edu /clustal/clustalhelp.html (1460 words)

	SEEBUGS Copyright Notice (Site not responding. Last check: 2007-10-21)
		Clustal W is freely available to the user community.
		Clustal W is now being distributed in a number of commercial packages.
		To help us safeguard future maintenance and development, commercial distributors of Clustal W are requested to donate a grant to the Clustal W authors which will be spent on Clustal W-related development.
	www.congenomics.com /microbes/COPYRIGHT.html (204 words)

	Similarity and Alignment Exercise (Site not responding. Last check: 2007-10-21)
		The essence of working with CLUSTAL is building a list of sequences that you wish to align.
		The most important considerations are that sequences must be of approximately the same length to avoid adding a lot of gaps at the ends and all of the sequences must be fairly closely related.
		By looking at the CLUSTAL output, you can see that some sequences extend beyond the rest at the 5' and 3' ends.
	www.med.nyu.edu /rcr/ASM/ex2.html (631 words)

	BSCI 380 Laboratory
		Today we will try out three multiple sequence alignment programs (gcg's pileup, the opensource clustal, and the web based t-coffee) and compare/contrast their outputs with the help of MacClade.
		Once clustal completes the alignment, you may open it in MacClade along with the guide tree in order to see if there are regions which "don't look good."
		Take some time to try out the different options, change the scoring matrix, change the output format, examine the low scoring columns, select a subset of sequences, remove their gaps and realign _just_ those sequences.
	www.wam.umd.edu /~abelew/bsci_380/msa.shtml (1042 words)

	HOMED V6.00 documentation
		Note that CLUSTAL pads the sequence with dashes so that you may wish to use the character replace function of HOMED's FIX option to restore blanks as padding characters.
		CLUSTAL is configured for up to 100 sequences of maximum length 5000 (including padding characters).
		The interface assumes that CLUSTAL alignment files conform to a format of 4 header lines (including a blank line), then blocks of aligned sequence with a leading blank, the sequence name, then each sequence from columns 17 to 76 inclusive.
	biochem.otago.ac.nz /resource/homed_doc.html (16266 words)

	Making a multiple sequence alignment (Site not responding. Last check: 2007-10-21)
		Clustal requires that all sequences be in the one file.
		Clustal will happily accept a GCG msf or rsf file.
		There is a facility in Clustal to re-align selected regions and to re-align selected sequences.
	www.molbiol.bbsrc.ac.uk /sequences/alignment.html (1432 words)

	CLUSTAL - Multiple Sequence Alignments - Manual
		The original Clustal was written by Des Higgins while he was a Post-Doc in the lab of Paul Sharp in the Genetics Department, Trinity College, Dublin 2, Ireland.
		The weight matrices used by Clustal V are shown in full in the Algorithms and References section of this documentation.
		Identities are highlighted and (if you use a PAM 250 matrix) positions in the alignment where all of the residues are "similar" to each other (PAM 250 score of 8 or more) are indicated.
	www.psc.edu /general/software/packages/clustal/manual/user_manual.html (5394 words)

	Clustal (Site not responding. Last check: 2007-10-21)
		Clustal W is a general purpose multiple sequence alignment program for DNA or proteins.
		Example of Clustal W setup: NOTE COLOR ALIGNMENT IS SET TO "YES".
		Next, multiple amino acid sequences can be entered at one time in the sequence window.
	webpages.marshall.edu /~spencer13/clustal.htm (84 words)

	Clustal W
		The program is also available with a graphical user interface, Clustal X.
		To run Clustal W at the Workshop on Molecular Evolution, type
		Clustal W is available for several computing platforms.
	workshop.molecularevolution.org /software/clustalw/index.php (156 words)

	(WO/2001/009304) POLYNUCLEOTIDES ENCODING AMINOLEVULINIC ACID BIOSYNTHETIC ENZYMES (Site not responding. Last check: 2007-10-21)
		Multiple alignment of the sequences was performed using the Clustal method of alignment (Higgins and Sharp (1989) CABIOS.
		A"substantial portion"of an amino acid or nucleotide sequence comprises an amino acid or a nucleotide sequence that is sufficient to afford putative identification of the protein or gene that the amino acid or nucleotide sequence comprises.
		The instant polypeptides (or portions thereof) may be produced in heterologous host cells, particularly in the cells of microbial hosts, and can be used to prepare antibodies to these proteins by methods well known to those skilled in the art.
	www.wipo.int /cgi-pct/guest/getbykey5?KEY=01/09304.010208&ELEMENT_SET=DECL (8042 words)

	Examples of CLUSTAL for the Sequence Analysis Resource (Site not responding. Last check: 2007-10-21)
		CLUSTAL is a package of multiple alignment programs.
		seq.aln, output file containing the multiple sequence alignment in clustal format.
		seq.dnd, output file containing the guide tree produced by clustal.
	www.psc.edu /general/software/seq/clustal/clustal.html (90 words)

	[CSS] Exercise: Wrapping Clustal W
		Clustal W is not installed globally on DAIMI, but I have compiled a version you can use.
		[mailund@dhcp-11-23-11 clustalw1.8]$./clustalw ************************************************************ **** CLUSTAL W (1.8) Multiple Sequence Alignments **** ************************************************************ 1.
		[mailund@dhcp-11-23-11 clustalw1.8]$./clustalw -align -infile=foo.fasta CLUSTAL W (1.8) Multiple Sequence Alignments Sequence format is Pearson Sequence 1: foobar1 15 bp Sequence 2: foobar2 15 bp Sequence 3: foobar3 13 bp Sequence 4: foobar4 13 bp Start of Pairwise alignments Aligning...
	www.daimi.au.dk /~mailund/css/clustalw-ex.html (1082 words)

	Distributed BLAST and Clustal W
		We will build distributed BLAST and Clustal W services and use these to position clones on the human genome, and build multiple alignments of the clones, respectively.
		You have already implemented a Clustal W wrapper in previous exercises, but we now want to make a distributed version.
		Exercise CLUSTALW.2: Build a Clustal W client — a script that takes the sequences to be aligned plus any options on the command line and performs the alignment using the distributed service.
	www.daimi.au.dk /~mailund/scripting2005/projects/project2.html (925 words)

	Sequence Alignments Using Clustal
		There are several parameters that you can set in clustal, and we will examine most of them using examples by trying them and seeing what happens.
		Click here to access the online clustal search page and here to read more about the parameters.
		Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice.
	bioinformatics.utmem.edu /clustal (797 words)

	Clustal X Coloring (Site not responding. Last check: 2007-10-21)
		The Clustal X coloring scheme in Multalign Viewer depends on both residue type and the pattern of conservation within a column.
		The Clustal X scheme is described in the color parameter file colprot.par.
		This scheme is encoded in Chimera and cannot be changed by users.
	www.cgl.ucsf.edu /chimera/1.2065/docs/ContributedSoftware/multalignviewer/cxcolor.html (306 words)

	UMSI: User's Guide - CLUSTAL X
		Clustal X is a windows interface for the ClustalW multiple sequence alignment program.
		On-line help can be found for clustalw.doc and Clustal X.
		To use UNIX version of program, you must initialize your environment including default paths and environmental variables which the package uses to access the programs and associated files.
	www.msi.umn.edu /software/clustalx (329 words)

	Converting CLUSTAL Format
		The sequence alignment outputs from CLUSTAL software often are given the default extension
		In a page-wide arrangement the sequence name is in the first column and a part of the sequence’s data is right justified.
		The CLUSTAL file above would be converted by
	www.megasoftware.net /WebHelp/inputdata_rh/rh_converting_clustal_format.htm (43 words)

	Clustal W Help
		Clustal W is a major re-write of the multiple alignment program Clustal V
		Thompson, J.D., Higgins, D.G. and Gibson, T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment
		CLUSTAL format output is a self explanatory alignment format.
	www.fut.es /~rhd/personal/TEMA4/CLUSTALW.HTM (4110 words)

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