probalign(1) [debian man page]
PROBALIGN(1) User Commands PROBALIGN(1) NAME
probalign - Align sequences in MFAFILE(s) and print result to standard output DESCRIPTION
PROBALIGN Version 1.4 (Nov 2010) aligns multiple protein sequences and prints to the standard output. Written by Satish Chikkagoudar and Usman Roshan using code from PROBCONS version 1.1 (written by Chuong Do) and based upon probA (written by Ulrike Muckstein). PROBALIGN 1.4 comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions. See the README file for details. Usage: probalign [OPTION]... [MFAFILE]... Description: Align sequences in MFAFILE(s) and print result to standard output -clustalw use CLUSTALW output format instead of MFA -v, --verbose report progress while aligning (default: off) -a, --alignment-order print sequences in alignment order rather than input order (default: off) -T, -temperature Sets the thermodynamic temperature parameter (default: 5 (for protein data mode), 1 ( for nucleotide data mode)). -score_matrix, --score_matrix Sets the type of scoring matrix used to calculate the posterior probabilities (default: gonnet_160, representing gonnet 160, refer README for details) -go, --gap-open This option can be used to specify the gap open parameter. The default for Gonnet 160 (protein) is 22 and nucleotide (simple matrix) is 4. -ge, --gap-extension This option can be used to specify the gap extension parameter. The default for Gonnet 160 (protein) is 1 and nucleotide (simple matrix) is 0.25. -nuc Specify this option to indicate that inputted sequences are nucleotide sequences -prot Specify this option to indicate that inputted sequences are protein sequences [DEFAULT] -showPP Outputs the posterior probabilities of alignment columns as a new sequence named Posterior Probabilities (The probability values are scaled to be between integers between 0 and 9). probalign 1.4 May 2011 PROBALIGN(1)
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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)