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maf-swap(1) [debian man page]

MAF-SWAP.PY(1)							   User Commands						    MAF-SWAP.PY(1)

NAME - changes the order of the sequences in MAF-format alignments SYNOPSIS [options] my-alignments.maf DESCRIPTION
Change the order of sequences in MAF-format alignments. OPTIONS
-h, --help show this help message and exit -n N move the Nth sequence to the top (default: 2) 199 May 2012 MAF-SWAP.PY(1)

Check Out this Related Man Page

LASTAL(1)							   User Commands							 LASTAL(1)

lastal - genome-scale comparison of biological sequences SYNOPSIS
lastal [options] lastdb-name fasta-sequence-file(s) DESCRIPTION
Find local sequence alignments. Score options (default settings): -r: match score (DNA: 1, protein: blosum62, 0<Q<5: 6) -q: mismatch cost (DNA: 1, protein: blosum62, 0<Q<5: 18) -p: file for residue pair scores -a: gap existence cost (DNA: 7, protein: 11, 0<Q<5: 21) -b: gap extension cost (DNA: 1, pro- tein: 2, 0<Q<5: 9) -c: unaligned residue pair cost (100000) -F: frameshift cost (off) -x: maximum score drop for gapped alignments (max[y, a+b*20]) -y: maximum score drop for gapless alignments (t*10) -z: maximum score drop for final gapped alignments (x) -d: minimum score for gapless alignments (e*3/5) -e: minimum score for gapped alignments (DNA: 40, protein: 100, 0<Q<5: 180) Cosmetic options (default settings): -h: show all options and their default settings -v: be verbose: write messages about what lastal is doing -o: output file -f: output format: 0=tabular, 1=maf (1) Miscellaneous options (default settings): -s: strand: 0=reverse, 1=forward, 2=both (2 for DNA, 1 for protein) -m: maximum multiplicity for initial matches (10) -l: minimum length for initial matches (1) -n: maximum number of gapless alignments per query position (infinity) -k: step-size along the query sequence (1) -i: query batch size (1 MiB if Q>0, else 16 MiB if j=0, else 128 MiB) -u: mask lowercase during extensions: 0=never, 1=gapless, 2=gapless+gapped but not final, 3=always (2 if lastdb -c and Q<5, else 0) -w: supress repeats inside exact matches, offset by this distance or less (1000) -G: genetic code file -t: 'temperature' for calculating probabilities (1/lambda) -g: 'gamma' parameter for gamma-centroid and LAMA (1) -j: output type: 0=match counts, 1=gapless, 2=redundant gapped, 3=gapped, 4=column ambiguity estimates, 5=gamma-centroid, 6=LAMA (3) -Q: input format: 0=fasta, 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina, 4=prb, 5=PSSM (0) REPORTING BUGS
Report bugs to: last (ATmark) cbrc (dot) jp LAST home page: lastal 199 May 2012 LASTAL(1)
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