9220
Comment: Treevolve: simulation of the evolution of DNA sequences
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9408
Treeplot is a conversion tool
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Deletions are marked like this. | Additions are marked like this. |
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||Tree export to graphical formats||[http://www.cnrs-gif.fr/pge/bioinfo/treeplot/ treeplot]||GPL||unofficial ([http://dept-info.labri.fr/~danjean/deb.html#treeplot ens-lyon])||free||no|| |
Integrated environments
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
[http://emboss.sourceforge.net/Jemboss/ Jemboss] |
GPL |
part of ["pkg-emboss"] |
free |
no |
[http://www.pasteur.fr/recherche/unites/sis/Pise/ Pasteur Institute Software Environment (Pise)] |
GPL |
complex |
free |
no |
many more on http://emboss.sourceforge.net/interfaces/, due to be prepared for Debian in the ["pkg-emboss"] effort.
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 (["pkg-emboss"]) |
GPL |
Debian-Bioinformatics |
vital |
yes (["pkg-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 |
[http://dnptrapper.sourceforge.net/ DNPTrapper] |
BSD |
depends on Qt and BerkeleyDB |
specialised on finishing |
no |
Database querying by alignment
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
NCBI blast |
free |
packaged (main) |
|
yes |
GPL |
easy ? |
popular alternative to BLAT |
no |
|
non-free |
no |
popular |
no |
|
[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 |
|
Academic, maybe closed source |
Hopeless: depends on phrap/cross_match |
unpackageable |
no |
|
[http://blast.wustl.edu/ wublast] |
non-free |
impossible |
unpackageable |
no |
Multiple alignment
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
t-coffee |
GPL |
packaged ([http://packages.debian.org/t-coffee main]) |
|
yes |
muscle |
Public domain |
packaged ([http://packages.debian.org/ main]) |
|
yes |
clustalw |
academic |
packaged ([http://packages.debian.org/clustalw non-free]) |
|
yes |
[http://dialign.gobics.de/ dialign] |
LGPL |
unofficial ([http://mentors.debian.net/debian/pool/main/d/dialign mentors]) |
|
yes |
[http://msa.cgb.ki.se/cgi-bin/msa.cgi kalign] |
GPL |
unofficial ([http://mentors.debian.net/debian/pool/main/k/kalign/ mentors]) |
|
no |
[http://probcons.stanford.edu/ probcons] |
public domain |
unofficial ([http://mentors.debian.net/debian/pool/main/p/probcons/ mentors]) |
|
no |
public domain |
ongoing ([http://bugs.debian.org/366321 ITP]) |
specialised in protein alignments |
no |
|
[http://contra.stanford.edu/contralign/ CONTRAlign] |
Public domain |
straightforward |
still in beta, wait for release |
no |
[http://dialign-t.gobics.de/ dialign-t] |
LGPL |
makefile is specific to ia32 |
better than dialign? |
no |
[http://biowiki.org/HandelPackage Handel] |
GPL |
part of the [http://sourceforge.net/projects/dart dart] package, which does not build out of the box on powerpc |
free |
no |
[http://evol-linux1.ulb.ac.be/ueg/ProAlign/ ?ProAlign] |
GPL |
depends on java |
has a graphical interface |
no |
[http://www.bio.inf.uni-jena.de/Software/MARNA/index.html marna] |
no licence |
depends on t-coffee and on the vienna RNA package |
Takes secondary structure of RNAs into account |
no |
mafft |
academic |
looks easy |
rare |
no |
prrn |
academic |
looks easy |
rare |
no |
[http://research.amnh.org/scicomp/projects/malign.php malign] |
unclear (discrepancies between files) |
impossible for the moment |
|
no |
saga |
non-redistributable |
impossible |
obsoleted by t-coffee? |
no |
|
|
|
no |
|
closed source? |
not without the source |
|
no |
Also, [http://www.drive5.com/qscore/ qscore], a program for scoring multiple alignments, is relevant. (but it has no license).
Multiple alignment viewers
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
seaview |
GPL |
packaged [(http://packages.debian.org/seaview contrib]) |
|
yes |
[http://msa.cgb.ki.se/cgi-bin/msa.cgi kalignvu] |
GPL |
easy, may depend on apache |
free |
no |
strap |
? |
depends on java |
|
no |
xced |
adademic |
no sources available |
rare |
no |
Phylogenetic analysis
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Tree display and manipulation |
njplot |
Artistic |
packaged ([http://packages.debian.org/njplot main]) |
|
yes |
Tree display |
?TreeView X |
GPL |
unofficial ([http://mentors.debian.net/debian/pool/main/t/treeviewx/ mentors]) |
|
yes |
Simulated evolution |
[http://evolve.zoo.ox.ac.uk/software.html?name=Treevolve Treevolve] |
not found |
unofficial [http://dept-info.labri.fr/~danjean/deb.html#treevolve ens-lyon] |
free |
no |
Tree export to graphical formats |
[http://www.cnrs-gif.fr/pge/bioinfo/treeplot/ treeplot] |
GPL |
unofficial ([http://dept-info.labri.fr/~danjean/deb.html#treeplot ens-lyon]) |
free |
no |
Confidence assessment |
GPL |
straightforward |
free |
no |
|
Visualisation of reconciliations |
[http://prime.sbc.su.se/primetv/ PriMETV] |
GPL |
depends on a [http://prime.sbc.su.se/primetv/plotutils.html patched version] of the GNU plotutils |
free |
no |
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 |
Tree display |
[http://www.treedyn.org/ ?TreeDyn] |
GPL |
Strangely, the sources are not available |
|
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 |
Calculating rates of evolution |
no licence found |
make fails |
|
no |
Other software
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Software suite |
[http://www.lecb.ncifcrf.gov/~toms/delila/delilaprograms.html delila] |
unkonwn |
depends on pascal |
|
no |
Base calling for ABI |
public domain |
looks easy |
the only free base caller for linux? |
no |
|
Command-line sequence manipulation |
["pkg-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 |
QA of mutiple alignments |
GPL |
easy |
free |
no |
|
Pairwise alignment |
[http://www.ebi.ac.uk/~guy/exonerate exonerate] |
LGPL |
[http://www.ebi.ac.uk/~guy/exonerate/debian/ in progress] |
free |
no |
Comparative sequence analysis |
FamilyJewelsII |
LGPL or GPL, have to look in the cvs |
depends on FLTK |
free |
no |
Graphical representation of sequence conservation |
[http://atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html ?PhyloGrapher] |
GPL |
depends on Tcl/Tk |
free |
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 |
Motif searching |
[http://zlab.bu.edu/glam/ glam] |
no licence found |
easy |
possible alternative to MEME |
no |
Motif representation |
[http://weblogo.berkeley.edu/ weblogo/seqlogo] |
BSD |
perl cgi |
free |
no |
Sequence comparisons |
[http://www.ebi.ac.uk/Wise2/ Wise2] |
GPL |
[http://envgen.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ bio-linux] |
free |
no |
Parser for blast output |
[ftp://ftp.pasteur.fr/pub/GenSoft/unix/alignment/Blast_tools/Html4blast/ html4blast] |
GPL |
depends on perl |
useful on local installations |
no |
Parser for blast output |
GPL |
C library, perl module |
says to be faste |
no |
|
Parser for blast output |
[http://www.pasteur.fr/~tekaia/HYG/blast2html blast2html] |
no licence |
trivial |
Not enough for a package. Group with other scripts? |
no |
display, manipulate and interconnect RNA data |
Public domain |
depends on java |
free |
no |
|
prediction of structural RNAs from sequence aligments |
Academic |
Depends on the Vienna RNA package |
|
no |
|
RNA secondary structure prediction and comparison |
[http://www.tbi.univie.ac.at/~ivo/RNA/ Vienna RNA package] |
Academic |
not for beginners |
|
no |
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