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clustalx(1) [debian man page]

CLUSTALW(1)						      General Commands Manual						       CLUSTALW(1)

NAME
clustalw - a multiple sequence alignment program SYNOPSIS
clustalw [options] DESCRIPTION
This manual page documents briefly the clustalx command. This manual page was written for the Debian GNU/Linux distribution because the original program does not have a manual page. Instead, it has other documentation; see below. clustalx is a windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results. The sequence alignment is displayed in a window on the screen. A versa- tile coloring scheme has been incorporated allowing you to highlight conserved features in the alignment. The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment. You can cut-and-paste sequences to change the order of the alignment; you can select a subset of sequences to be aligned; you can select a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. SEE ALSO
Files in /usr/share/doc/clustalx contain a lot of details. The Web page <http://www.clustal.org/> is also helpful. AUTHOR
This manual page was written by Andreas Tille <tille@debian.org>, for the Debian GNU/Linux system (but may be used by others). Manual for clustalw 2003 July 1 CLUSTALW(1)

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POA(1)																	    POA(1)

NAME
poa - align a set of sequences or alignments. SYNOPSIS
poa [OPTIONS] [MATRIXFILE] One of the -read_fasta, -read_msa, or -read_msa_list arguments must be used, since a sequence or alignment file is required. DESCRIPTION
POA is Partial Order Alignment, a fast program for multiple sequence alignment (MSA) in bioinformatics. Its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment. Partial order alignment is an approach to MSA, which can be combined with existing methods such as progressive alignment. POA optimally aligns a pair of MSAs and which therefore can be applied directly to progressive alignment methods such as CLUSTAL. For large alignments, Progressive POA is 10 to 30 times faster than CLUSTALW. EXAMPLES
poa -read_fasta multidom.seq -clustal m.aln blosum80.mat On Debian systems, poa can be tested using the following command: poa -read_fasta /usr/share/doc/poa/examples/multidom.seq -clustal /dev/stdout -v /usr/share/poa/blosum80.mat OPTIONS
INPUT -read_fasta FILE Read in FASTA sequence file. -read_msa FILE Read in MSA alignment file. -read_msa2 FILE Read in second MSA file. -subset FILE Filter MSA to include list of seqs in file. -subset2 FILE Filter second MSA to include list of seqs in file. -remove FILE Filter MSA to include list of seqs in file. -remove2 FILE Filter second MSA to include list of seqs in file. -read_msa_list FILE Read an MSA from each filename listed in file. -tolower Force FASTA/MSA sequences to lowercase (nucleotides in our matrix files). -toupper Force FASTA/MSA sequences to UPPERCASE (amino acids in our matrix files). ALIGNMENT -do_global Do global alignment. -do_progressive Perform progressive alignment using a guide tree built by neighbor joining from a set of sequence-sequence similarity scores. -read_pairscores FILE Read tab-delimited file of similarity scores (If not provided, scores are constructed using pairwise sequence alignment.) -fuse_all Fuse identical letters on align rings. ANALYSIS -hb Perform heaviest bundling to generate consensi. -hbmin VALUE Include in heaviest bundle sequences with percent ID (as a fraction) >= VALUE. OUTPUT -pir FILE Write out MSA in PIR format. -clustal FILE Write out MSA in CLUSTAL format. -po FILE Write out MSA in PO format. -preserve_seqorder Write out MSA with sequences in their input order. -printmatrix LETTERS Print score matrix to stdout. -best Restrict MSA output to heaviest bundles (PIR only). -v Run in verbose mode (e.g. output gap penalties). REFERENCE
Please cite Grasso C, Lee C.(2004) Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics. 2004 Jul 10;20(10):1546-56. Epub 2004 Feb 12. SEE ALSO
The homepage of POA is http://www.bioinformatics.ucla.edu/poa COPYRIGHTS
Copyright (C) 2001, 2006 Christopher Lee <leec@mbi.ucla.edu>. POA is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation. This manual page was written by Charles Plessy <charles-debian-nospam@plessy.org> for the Debian(TM) system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. COPYRIGHT
Copyright (C) 2006 Charles Plessy september 26, 2006 POA(1)
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