Short explanation:
This page lists programs which are usefull to the field of sequence analysis. It is mostly software related to sequence alignment, phylogeny, motif finding, and sequence manipulation.
Most column names are self-explanatory. When a licence is listed as "Academic", it means that the program is only free of charge for academic, non-profit research, which makes non-compliant to the DebianFreeSoftwareGuidelines. "Packaging" gives cues about the difficulty of the packaging, or indicates that the program has already been packaged. "Importance" gives cues about what to package first. That is why programs already packaged have nothing written there: it does not mean that they are not important!. "Listed on... " records whether the program is listed on the official DebianMed website.
Integrated environments
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
[http://emboss.sourceforge.net/Jemboss/ Jemboss] |
GPL |
part of ["pkg-emboss"] |
free |
no |
[http://wemboss.sourceforge.net/ wemboss] |
GPL |
perl CGI? |
free |
no |
[http://www.pasteur.fr/recherche/unites/sis/Pise/ Pasteur Institute Software Environment (Pise)] |
GPL |
complex |
free |
no |
GPL |
javascript and html |
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"]) |
[http://www.littlest.co.uk/software/bioinf/index.html ?TraceView] |
Not found |
Depends on JAVA |
|
no |
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
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
NCBI blast |
free |
packaged (main) |
|
yes |
HMMER |
GPL |
packaged (main) |
|
yes |
GPL |
easy ? |
popular alternative to BLAT |
no |
|
GPL |
big package |
free |
no |
|
[http://infernal.janelia.org/ Infernal] |
GPL |
big package |
free |
no |
GPL |
Depends on squid |
free |
no |
|
[http://exon.umdnj.edu/software/RSmatch/ RSmatch] |
not found |
Depends on java and recommends the Vienna package |
|
no |
[http://tagc.univ-mrs.fr/erpin/ erpin] |
not found |
looks easy |
|
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 |
Pairwise alignment
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
NCBI blast |
public domain |
packaged ([http://packages.debian.org/unstable/science/blast2 main]) |
|
yes |
[http://contra.stanford.edu/contralign/ CONTRAlign] |
Public domain |
straightforward |
free |
yes |
[http://neobio.sourceforge.net/ ?NeoBio] |
GPL |
depends on java |
free, has GUI and command line, and supports multiple algorithms |
no |
[http://jaligner.sourceforge.net/ jaligner] |
GPL |
depends on java |
has a GUI |
no |
[http://bioinfo.lifl.fr/yass/ Yass] |
GPL |
trivial |
free |
no |
[http://foldalign.kvl.dk/software/index.html foldalign] |
GPL |
should be easy |
free |
no |
not found |
trivial |
many alternatives... benchmark ? |
no |
|
[http://www.well.ox.ac.uk/ariadne/ ariadne] |
[http://www.well.ox.ac.uk/ariadne/disclaimer.shtml disclaimer] |
build failed on ppc |
has a method for determining statistical significance |
no |
[http://www.ebi.ac.uk/~guy/exonerate exonerate] |
LGPL |
[http://www.ebi.ac.uk/~guy/exonerate/debian/ in progress] |
free |
no |
lalign |
academic |
part of the fasta package |
unredistributable (see above) |
no |
prss |
academic |
part of the fasta package |
unredistributable (see above) |
no |
[http://globin.cse.psu.edu/java/laj/ laj] (viewer) |
not found |
depends on java |
|
no |
[http://pbil.univ-lyon1.fr/software/lalnview.html lalnview] (viewer) |
GPL |
depends on fltk and pdflib |
free (contrib) |
no |
Multiple alignment
The multiple alignment programs have been transferred to a separate page, SequenceAlignment.
Also, [http://www.drive5.com/qscore/ qscore], a program for scoring multiple alignments, is relevant. (but it has no license).
Multiple alignment viewers and editors
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 |
GPL |
depends on java |
free |
no |
|
[http://www.jalview.org jalview] |
GPL |
depends on java |
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 |
packaged ([http://packages.debian.org/treeviewx main]) |
|
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 |
Simulated evolution |
[http://evolve.zoo.ox.ac.uk/software.html?name=Seq-Gen Seq-Gen] |
BSD |
unofficial ([http://dept-info.labri.fr/~danjean/deb.html#seqgen 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 |
Tree inference |
[http://mrbayes.csit.fsu.edu/ ?MrBayes] |
GPL |
easy |
free and popular |
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 |
depends on Tcl/Tk |
looks comprehensive |
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 |
|
Selecting evolution model |
GPL |
depends on java |
free |
no |
|
Calculating rates of evolution |
no licence found |
make fails |
|
no |
|
Detects families |
[http://bioinformatics.org/branchclust/ ?BranchClust] |
No licence found |
Depends on Perl |
|
no |
Merges trees into a graph |
[http://www.splitstree.org/ Splitstree4] |
|
Depends on java |
|
no |
Merges trees into a graph |
[http://www-ab.informatik.uni-tuebingen.de/software/splits/welcome.html Splitstree] |
|
Depends on Tk |
|
no |
Motif detection
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
[http://www.biozentrum.unibas.ch/~nimwegen/cgi-bin/phylogibbs.cgi ?PhyloGibbs] |
GPL |
maybe easy |
free |
no |
Artistic |
looks easy |
free |
no |
|
[http://jakob.genetik.uni-koeln.de/bioinformatik/people/nora/nora.html ?CisPlusFinder] |
LGPL |
depends on libtie-ixhash-perl, looks easy |
free |
no |
[http://zlab.bu.edu/glam/ glam] |
no licence found |
easy |
possible alternative to MEME |
no |
[http://meme.sdsc.edu/meme/intro.html MEME and MAST] |
academic |
[http://www.scientificcomputing.net/debian/packages/meme/ unofficial] [http://tp12.pzr.uni-rostock.de/~moeller/debian/meme/ packages] |
popular |
no |
[http://www.bioinf.uni-freiburg.de/~hiller/MEMERIS/ MEMERIS] |
Academic |
builds fine |
Will not be packaged unless requested |
no |
[http://faculty.cs.tamu.edu/shsze/motifenumerator/ ?MotifEnumerator] |
not found |
one .c file only! |
|
no |
[http://atlas.med.harvard.edu/ AlignACE] |
[http://atlas.med.harvard.edu/download/index.html Harvard EULA] |
check with DebianLegal first |
|
no |
Academic |
Sources not available |
maybe too closed |
no |
|
[http://bioinformatics.ucd.ie/shields/software/slimdisc/ SLIMDisc] |
not found |
Depends on Python |
|
no |
Also, the following software is related:
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Motif representation |
[http://weblogo.berkeley.edu/ weblogo/seqlogo] |
BSD |
perl cgi |
free |
no |
Secondary structure of nucleic acids
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
display, manipulate and interconnect RNA data |
Public domain |
depends on java |
free |
no |
|
RNA secondary structure |
[http://contra.stanford.edu/contrafold/download.html CONTRAfold] |
BSD |
looks easy |
free |
no |
prediction of structural RNAs from sequence aligments |
[http://www.tbi.univie.ac.at/~ivo/RNA/COPYING.html Academic] |
Depends on the Vienna RNA package |
|
no |
|
Predicting structural motifs in aligned nucleotide sequences |
[http://www.tigem.it/Research/Personal%20Web%20Page_files/dibernardo/Website/frame_software.htm ddbRNA] |
not found |
depends on java |
|
no |
RNA secondary structure prediction and comparison |
[http://www.tbi.univie.ac.at/~ivo/RNA/ Vienna RNA package] |
Academic |
not for beginners |
|
no |
RNA secondary structure |
[http://bibiserv.techfak.uni-bielefeld.de/download/tools/rnashapes.html RNAshapes] |
Same as Vienna package (non-free) |
Mixture of C and Java |
|
no |
Prediction of secondary structure from multiple alignment |
[http://rna.cyanolab.de/ RNAlishape] |
No redistribution fee except media costs |
Depends on Haskell |
|
no |
Nucleic acid folding |
[http://www.bioinfo.rpi.edu/applications/hybrid/download.php UNAfold] |
[http://www.bioinfo.rpi.edu/applications/hybrid/license.php academic] |
looks easy |
|
no |
Other software
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Sequence comparisons |
[http://www.ebi.ac.uk/Wise2/ Wise2] |
GPL |
packaged ([http://packages.debian.org/unstable/science/wise main]) |
|
no |
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 |
|
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 |
Sequence comparisons |
[http://www.ebi.ac.uk/Wise2/ Wise2] |
GPL |
packaged [http://packages.debian.org/unstable/science/wise main] |
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 |
Prediction of coding sequence |
[http://geta.life.uiuc.edu/~gary/programs/CRITICA.html Critica] |
GPL |
not tried |
free |
no |
Masking low-complexity strings |
No licence |
trivial |
used in GCG |
no |
|
Masking low-complexity strings |
No licence |
trivial |
advertised in FASTA |
no |
|
Matching EST to genome |
[http://www.well.ox.ac.uk/~rmott/ESTGENOME/est_genome.shtml est_genome] |
not found |
looks simple |
an alternative, sim4, is already packaged |
no |
Protein analysis |
[http://webclu.bio.wzw.tum.de/prompt/ prompt] |
GPL |
depends on R, blast2, java |
free |
no |
Protein analysis |
[http://www.evolvingcode.net:8080/aaindex/tools/ Amino Acid Explorer] |
Apache |
depends on java |
free |
no |
Cis-elements prediction |
Not found |
various sub-components |
|
no |
|
Semi-automated sequence analysis |
[http://www.ncbi.nlm.nih.gov/CBBresearch/Walker/SEALS/ SEALS] |
Public domain |
Depends on webbrowser, hmmer, clustalw, ncbi-toolkit, blast, and other programs |
free |
no |
ORF finding |
[http://www.cbs.dtu.dk/services/VirtualRibosome/download.php Virtual Ribosome] |
GPL |
Depends on python |
free |
no |
ORF finding |
Public domain |
optionaly depends on webserver |
free |
no |
|
ORF finfing |
GPL |
seems simple to package |
free |
no |
|
CpG islands prediction |
[http://bioinfo2.ugr.es/CpGcluster/ ?CpGcluster] |
not found |
perl script, could be grouped with others |
|
no |
Pretty printing of aligmnents |
[http://espript.ibcp.fr/ESPript/ESPript/ ESPript] |
non free (commercial licence is 1000 euros) |
fortran program |
not packaged unless requested |
no |
Structural alignment |
[http://cl.sdsc.edu/ CE] |
Academic |
should be easy |
not packaged unless requested |
no |
snoRNA discovery |
[http://genelab.zsu.edu.cn/HSsnoRNA.html snoSeeker] |
not found |
depends on Vienna and Mfold |
would be in "contrib" |
no |
miRNA target discovery |
[http://www.microrna.org/miranda_new.html miRanda] |
GPL |
Depends on the Vienna package |
would be in "contrib" |
no |
conserved elements discovery |
[http://tavazoielab.princeton.edu/fastcompare/ ?FastCompare] |
looks trivial |
free |
no |
|
graphical representation |
[http://athena.bioc.uvic.ca/workbench.php?tool=graphdna&db= graphDNA] |
website says opensource |
depends on java |
free? |
no |
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