Trace viewers
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
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.
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 |
3D Trees |
GPL |
java knowledge needed |
free, looks powerful |
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 |
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