Artemis 16.0 freeware
Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.
Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format.
|Author||Wellcome Trust Sanger Institute|
|OS||Windows 2000, Windows 2003, Windows XP, Windows Vista, Windows 7, Linux, Mac OS X, Java|
|Installation||Instal And Uninstall|
|Keywords||DNA Sequence, Sequence Viewer, Sequence Annotation, DNA, Sequence, Annotation|
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|16.0||Sep 1, 2013||New Release||Add 'Features Within Selection' option to the 'Select' menu to select
features that are contained by a selected base range.
Saving an entry as EMBL submission has an option now to remove products
from CDS features with a pseudogene qualifier.
From the 'View' menu added 'Adjust panel heights...' option in ACT
for adjusting their heights (BAM, VCF, plots, comparisons) by giving
them different weights in order to distribute the space between each
Added ability to hide graph lines. Right click on the graph to get the
popup menu and select 'Configure...'. Then use the 'Line size' slider
to reduce the size of the line(s) that you want to hide to zero.
Labels can optionally be added to the header of base position plots
and these are used in the legend, e.g.
# colour 5:150:55 255:0:0 0:255:0 0:0:255 100:100:100 50:150:50
# label lab1 lab2 lab3 lab4 lab5 lab6
176 2204.8 848.23 0 0 0 536.04
|15.0||Sep 1, 2013||New Release||Multiple BAM panels can be opened using the bamClone flag this is used with
the -Dbam flag:
art -Dbam='/pathToFile/file1.bam,/pathToFile/file2.bam' -DbamClone=n
(where n is an integer greater than 1). All BAM files are then shown in each
panel. Alternatively the following will open BAM files in separate panels
art -Dbam1=fileA.bam -Dbam2=fileB.bam
Add SVG (scalable vector graphics) support for Artemis, ACT and DNAPlotter.
Option added to adjust VCF row height.
Add support for indexed user graphs using tabix. For example file.plot is a tab
delimited file with column 1 containing the sequence name and column 2 the
(grep ^"#" file.plot; grep -v ^"#" file.plot | sort -k1,1 -k2,2n) | bgzip > sorted.plot.gz ;
tabix -s 1 -b 2 -e 2 sorted.plot.gz
Option added to show or hide the average line in the graphs.
BAM coverage heatmap view added.
Add Rfam sequence search from the RUN menu.
|14.0||Jun 25, 2012||New Release||Add options in the navigator for searching the forward and
reverse strands individually for base / amino acid patterns.
Add an option to the navigator for searching for matches that
overlap a selected region or feature.
New translation table 24 (Pterobranchia mitochondrial) added.
If the BAM index file is missing then Artemis uses the picard library to
attempt to create the index.
Variant (VCF / BCF) filtering now uses the meta-data in the header to
enable filtering based on INFO, FILTER and FORMAT columns.
Shortcut changes made in the 'Preferences' menu are saved between sessions (the
shortcut_cache flag in the options file can be used to turn this on/off).
More support for GTF format to show CDS and exons as joined features.
BAM record list option added to display as a list the reads and their
Add options for loading graph, BAM and VCF files into ACT from the
command line. Numbers are used to associate the file with a particular