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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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LASTAL(1) User Commands LASTAL(1) NAME
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: http://last.cbrc.jp/ lastal 199 May 2012 LASTAL(1)