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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CD-HIT-EST(1) User Commands CD-HIT-EST(1) NAME
cdhit-est - run CD-HIT algorithm on RNA/DNA sequences SYNOPSIS
cdhit-est [Options] DESCRIPTION
====== CD-HIT version 4.6 (built on Apr 26 2012) ====== Options -i input filename in fasta format, required -o output filename, required -c sequence identity threshold, default 0.9 this is the default cd-hit's "global sequence identity" calculated as: number of identical amino acids in alignment divided by the full length of the shorter sequence -G use global sequence identity, default 1 if set to 0, then use local sequence identity, calculated as : number of identical amino acids in alignment divided by the length of the alignment NOTE!!! don't use -G 0 unless you use alignment coverage controls see options -aL, -AL, -aS, -AS -b band_width of alignment, default 20 -M memory limit (in MB) for the program, default 800; 0 for unlimitted; -T number of threads, default 1; with 0, all CPUs will be used -n word_length, default 10, see user's guide for choosing it -l length of throw_away_sequences, default 10 -d length of description in .clstr file, default 20 if set to 0, it takes the fasta defline and stops at first space -s length difference cutoff, default 0.0 if set to 0.9, the shorter sequences need to be at least 90% length of the representative of the cluster -S length difference cutoff in amino acid, default 999999 if set to 60, the length difference between the shorter sequences and the representative of the cluster can not be bigger than 60 -aL alignment coverage for the longer sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence -AL alignment coverage control for the longer sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the alignment must be >= 340 (400-60) residues -aS alignment coverage for the shorter sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence -AS alignment coverage control for the shorter sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the alignment must be >= 340 (400-60) residues -A minimal alignment coverage control for the both sequences, default 0 alignment must cover >= this value for both sequences -uL maximum unmatched percentage for the longer sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tailing gaps) must not be more than 10% of the sequence -uS maximum unmatched percentage for the shorter sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tail- ing gaps) must not be more than 10% of the sequence -U maximum unmatched length, default 99999999 if set to 10, the unmatched region (excluding leading and tailing gaps) must not be more than 10 bases -B 1 or 0, default 0, by default, sequences are stored in RAM if set to 1, sequence are stored on hard drive it is recommended to use -B 1 for huge databases -p 1 or 0, default 0 if set to 1, print alignment overlap in .clstr file -g 1 or 0, default 0 by cd-hit's default algorithm, a sequence is clustered to the first cluster that meet the threshold (fast clus- ter). If set to 1, the program will cluster it into the most similar cluster that meet the threshold (accurate but slow mode) but either 1 or 0 won't change the representatives of final clusters -r 1 or 0, default 1, by default do both +/+ & +/- alignments if set to 0, only +/+ strand alignment -mask masking letters (e.g. -mask NX, to mask out both 'N' and 'X') -match matching score, default 2 (1 for T-U and N-N) -mismatch mismatching score, default -2 -gap gap opening score, default -6 -gap-ext gap extension score, default -1 -bak write backup cluster file (1 or 0, default 0) -h print this help Questions, bugs, contact Limin Fu at l2fu@ucsd.edu, or Weizhong Li at liwz@sdsc.edu For updated versions and information, please visit: http://cd-hit.org cd-hit web server is also available from http://cd-hit.org If you find cd-hit useful, please kindly cite: "Clustering of highly homologous sequences to reduce thesize of large protein database", Weizhong Li, Lukasz Jaroszewski & Adam Godzik. Bioinformatics, (2001) 17:282-283 "Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences", Weizhong Li & Adam Godzik. Bioinformatics, (2006) 22:1658-1659 cd-hit-est 4.6-2012-04-25 April 2012 CD-HIT-EST(1)