Chromatogram viewers
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
[http://neelix.molbiol.ox.ac.uk:8080/userweb/mchan/stars/ STARS] |
GPL |
depends on Staden |
free |
no |
trev (Staden) |
BSD |
packaging the whole Staden seems difficlut |
vital |
yes (Staden) |
abiview (Emboss) |
GPL |
Debian-Bioinformatics |
vital |
yes (emboss) |
Abiview has a better command line interface, and trev has a better gui.
Sequence assembly
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
[http://seq.cs.iastate.edu/ CAP3] |
academic |
maybe closed source |
not a lot of alternatives |
no |
[http://www.atgc.org/Py_ContigViewer/ ?ContigViewer] |
GPL |
depends on python |
Works on CAP3 output |
no |
Multiple alignment
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
t-coffee |
GPL |
main |
free |
yes |
clustalw |
academic |
non-free |
very popular |
yes |
muscle |
Public domain |
main |
free |
no |
mafft |
academic |
looks easy |
rare |
no |
prrn |
academic |
looks easy |
rare |
no |
dialign |
proprietary ? |
no |
rare ? |
no |
Phylogenetic analysis
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Tree display and manipulation |
njplot |
Artistic |
main |
free |
yes |
Tree display |
?TreeView X |
GPL |
in progress |
SVG output |
yes |
Tree display |
Phylodendron |
pre-release of 1996 |
java knowledge needed |
nice output |
no |
Tree display and manipulation |
ATV |
[http://www.genetics.wustl.edu/eddy/forester/forester_distribution/LICENSE.txt Forester] |
java knowledge needed |
looks powerful |
no |
Coloring tree |
[http://www.biomedcentral.com/1471-2105/7/79/abstract ?PhyloView] |
GPL |
perl cgi knowledge needed |
free |
no |
3D Trees |
GPL |
java knowledge needed |
free, looks powerful |
no |
|
Tree inference |
?MrBayes |
GPL |
|
free |
no |
Other software
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Command-line sequence manipulation |
EMBOSS |
L/GPL |
unofficial |
vital |
yes |
Multiple alignment (graphic) |
pipmaker |
GPL |
looks easy |
free alternative to vista? |
no |
Multiple alignment (graphic) |
vista |
academic |
downloading sources require registration |
popular |
no |
Multiple alignment (graphic) |
mussa |
GPL |
looks easy |
free |
no |
Comparative sequence analysis |
FamilyJewelsII |
LGPL or GPL, have to look in the cvs |
depends on FLTK |
free |
no |
Alignment editor |
xced |
adademic |
no sources available |
rare |
no |
Graphical representation of sequence conservation |
[http://atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html ?PhyloGrapher] |
GPL |
depends on Tcl/Tk |
free |
no |
Database querying by sequence alignment |
non-free |
no |
popular |
no |
|
Database querying by sequence alignment |
[ftp://ftp.virginia.edu/pub/fasta/COPYRIGHT academic] |
[http://lists.debian.org/debian-med/2005/05/msg00028.html upstream does not want], but there is one in [http://envgen.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ bio-linux] |
popular |
no |
|
Motif searching |
[http://meme.sdsc.edu/meme/intro.html MEME and MAST] |
academic |
[https://www.bioinformatics.uwaterloo.ca/wiki/index.php?refs=Local%20Debian%20Repository private repository] |
popular |
no |
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