lastex(1) [debian man page]

LASTEX(1)							   User Commands							 LASTEX(1)

NAME

       lastex - Calculate expected numbers of alignments for random sequences.

DESCRIPTION

       Usage:  lastex  [options]  reference-counts-file  query-counts-file  [alignments-file]  Calculate expected numbers of alignments for random
       sequences.

       Options (default settings): -h: show all options and their default settings -s: strands (2 for DNA, 1 for protein) -r: match score    (DNA:
       1,  protein:  blosum62) -q: mismatch cost (DNA: 1, protein: blosum62) -p: file for residue pair scores -a: gap existence cost (DNA: 7, pro-
       tein: 11) -b: gap extension cost (DNA: 1, protein:  2) -g: do calculations for gapless alignments -y: find the expected	number	of  align-
       ments with score >= this -E: maximum expected number of alignments -z: calculate the expected number of alignments per:

	      0  =  reference  counts file / query counts file 1 = reference counts file / each query sequence 2 = each reference sequence / query
	      counts file 3 = each reference sequence / each query sequence (0)

REPORTING BUGS

       Report bugs to: last (ATmark) cbrc (dot) jp
       LAST home page: http://last.cbrc.jp/

lastex 199							     May 2012								 LASTEX(1)

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)