.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH LASTAL "1" "October 2014" "lastal 490" "User Commands"
.SH NAME
lastal \- genome-scale comparison of biological sequences
.SH SYNOPSIS
.B lastal
[\fI\,options\/\fR] \fI\,lastdb-name fasta-sequence-file(s)\/\fR
.SH DESCRIPTION
Find local sequence alignments.
.PP
Score options (default settings):
\fB\-r\fR: match score   (DNA: 1, 0<Q<5:  6)
\fB\-q\fR: mismatch cost (DNA: 1, 0<Q<5: 18)
\fB\-p\fR: match/mismatch score matrix (protein\-protein: BL62, DNA\-protein: BL80)
\fB\-a\fR: gap existence cost (DNA: 7, protein: 11, 0<Q<5: 21)
\fB\-b\fR: gap extension cost (DNA: 1, protein:  2, 0<Q<5:  9)
\fB\-A\fR: insertion existence cost (a)
\fB\-B\fR: insertion extension cost (b)
\fB\-c\fR: unaligned residue pair cost (off)
\fB\-F\fR: frameshift cost (off)
\fB\-x\fR: maximum score drop for gapped alignments (max[y, e\-1])
\fB\-y\fR: maximum score drop for gapless alignments (t*10)
\fB\-z\fR: maximum score drop for final gapped alignments (x)
\fB\-d\fR: minimum score for gapless alignments (min[e, t*ln(1000*refSize/n)])
\fB\-e\fR: minimum score for gapped alignments (DNA: 40, protein: 100, 0<Q<5: 180)
.PP
Cosmetic options (default settings):
\fB\-h\fR: show all options and their default settings
\fB\-v\fR: be verbose: write messages about what lastal is doing
\fB\-f\fR: output format: 0=tabular, 1=maf (1)
.PP
Miscellaneous options (default settings):
\fB\-s\fR: strand: 0=reverse, 1=forward, 2=both (2 for DNA, 1 for protein)
\fB\-T\fR: type of alignment: 0=local, 1=overlap (0)
\fB\-m\fR: maximum initial matches per query position (10)
\fB\-l\fR: length threshold for initial matches (1 if \fB\-j0\fR, else infinity)
\fB\-n\fR: maximum gapless alignments per query position (infinity if m=0, else m)
\fB\-C\fR: culling limit for gapless alignments (off)
\fB\-k\fR: step\-size along the query sequence (1)
\fB\-i\fR: query batch size (8 KiB, unless there are multiple lastdb volumes)
\fB\-u\fR: mask lowercase during extensions: 0=never, 1=gapless,
.IP
2=gapless+gapped but not final, 3=always (2 if lastdb \fB\-c\fR and Q<5, else 0)
.PP
\fB\-w\fR: supress repeats inside exact matches, offset by this distance or less (1000)
\fB\-G\fR: genetic code file
\fB\-t\fR: 'temperature' for calculating probabilities (1/lambda)
\fB\-g\fR: 'gamma' parameter for gamma\-centroid and LAMA (1)
\fB\-j\fR: output type: 0=match counts, 1=gapless, 2=redundant gapped, 3=gapped,
.IP
4=column ambiguity estimates, 5=gamma\-centroid, 6=LAMA (3)
.PP
\fB\-Q\fR: input format: 0=fasta, 1=fastq\-sanger, 2=fastq\-solexa, 3=fastq\-illumina,
.IP
4=prb, 5=PSSM (0)
.SH "REPORTING BUGS"
Report bugs to: last\-align (ATmark) googlegroups (dot) com
.br
LAST home page: http://last.cbrc.jp/