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Geneious 4.5.4 (Default branch)
01-28-2009
Geneious is an integrated bioinformatics tool suite for manipulating, finding, sharing, and exploring biological data such as linear and circular DNA sequences, proteins, phylogenies, chromatograms, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis, restriction analysis, contig assembly, access to biological databases at NCBI and elsewhere (PubMed, Nucleotide, PopSet, SNP, Structure, PFAM, etc.), BLAST, and more. It includes an API for creating your own plugins.License: Other/Proprietary License with Free TrialChanges:|
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clustalo(1) USER COMMANDS clustalo(1) NAME
clustalo - General purpose multiple sequence alignment program for proteins SYNOPSIS
clustalo [-h] DESCRIPTION
Clustal-Omega is a general purpose multiple sequence alignment (MSA) program for proteins. 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 can only align protein sequences but not DNA/RNA sequences. It is envisioned that DNA/RNA will become available in a future version. USAGE
Tool usage is available in /usr/share/doc/clustalo/README. DEVELOPMENT
Headers and libraries are available in libclustalo-dev package. CITING
Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Soding J, Thompson JD, Higgins DG (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7. AUTHOR
Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging Conway Institute UCD Dublin (clustalw (at) ucd.ie) - clustalo version 1.0.3 December 14, 2011 clustalo(1)