.TH ART 1 "February 2014"

.SH NAME
art \- Artemis genome browser and annotation tool

.SH SYNOPSIS
.B art
.RI [ options ]
.I SEQUENCE_FILE
.RI [ +FEATURE_FILE ...]

.SH OPTIONS
        SEQUENCE_FILE                  An EMBL, GenBank, FASTA, or GFF3 file
        FEATURE_FILE                   An Artemis TAB file, or GFF file

        -options FILE                  Read a text file of options from FILE
        -debug                         Run using the debugging JVM instead
        -fast | -fast64                Use the FastVM (hp Tru64 UNIX) with 32/64 bit pointers

        -Dblack_belt_mode=?            Keep warning messages to a minimum [true,false]
        -Doffset=XXX                   Open viewer at base position XXX [integer >= 1]
        -Duserplot=FILE[,FILE2]        Open one or more userplots
        -Dloguserplot=FILE[,FILE2]     Open one or more userplots, take log(data)
        -Dbam=FILE[,FILE2,...]         Open one or more BAM, VCF or BCF files
        -DbamClone=n                   Open all BAMs in multiple (n > 1) panels
        -Dbam[1,2,..]=FILE[,FILE2,..]  Open BAMs in separate panels
        -Dshow_snps                    Show SNP marks in BamView
        -Dshow_snp_plot                Open SNP plot in BamView
        -Dshow_cov_plot                Open coverage plot in BamView
        -Dshow_forward_lines=?         Hide/show forward frame lines [true,false]
        -Dshow_reverse_lines=?         Hide/show reverse frame lines [true,false]
        -Dchado="h:p/d?u"              Get Artemis to open this CHADO database
        -Dread_only                    Open CHADO database read-only
.SH EXAMPLES
        % art AJ006275.embl 
        % art contigs.fa +annotation.gff +islands.tab
        % art -Dblack_belt_mode=true -Dbam=ecoli_hiseq.bam E_coli_K12.gbk
        % art -Duserplot=repeatmap.plot,geecee.plot Plasmid.gff3
.SH SEE ALSO
        http://www.sanger.ac.uk/resources/software/artemis/

.BR act (1),
.BR dnaplotter (1)