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 |
GPL |
part of ?pkg-emboss |
free |
|
GPL |
perl CGI? |
free |
|
GPL |
complex |
free |
|
GPL |
javascript and html |
free |
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 |
GPL |
depends on Staden |
free |
|
trev (Staden) |
BSD |
packaging the whole Staden seems difficlut |
vital |
Not found |
Depends on JAVA |
|
Abiview has a better command line interface, and trev has a better gui.
Sequence assembly
Program |
Licence |
Packaging |
Importance |
GPL |
depends on python |
Works on CAP3 output |
|
BSD |
depends on Qt and BerkeleyDB |
specialised on finishing |
Database querying
Program |
Licence |
Packaging |
Importance |
GPL |
easy ? |
popular alternative to BLAT |
|
GPL |
big package |
free |
|
GPL |
Depends on squid |
free |
|
not found |
Depends on java and recommends the Vienna package |
|
|
not found |
looks easy |
|
|
non-free |
no |
popular |
|
upstream does not want, but there is one in bio-linux |
popular |
||
Academic, maybe closed source |
Hopeless: depends on phrap/cross_match |
unpackageable |
|
non-free |
impossible |
unpackageable |
Pairwise alignment
Program |
Licence |
Packaging |
Importance |
Public domain |
straightforward |
free |
|
GPL |
depends on java |
free, has GUI and command line, and supports multiple algorithms |
|
GPL |
depends on java |
has a GUI |
|
GPL |
trivial |
free |
|
GPL |
should be easy |
free |
|
not found |
trivial |
many alternatives... benchmark ? |
|
build failed on ppc |
has a method for determining statistical significance |
||
lalign |
academic |
part of the fasta package |
unredistributable (see above) |
prss |
academic |
part of the fasta package |
unredistributable (see above) |
BSD |
easy |
free and popular |
|
laj (viewer) |
not found |
depends on java |
|
lalnview (viewer) |
GPL |
depends on fltk and pdflib |
free (contrib) |
Multiple alignment
The multiple alignment programs have been transferred to a separate page, SequenceAlignment.
Also, qscore, a program for scoring multiple alignments, is relevant. (but it has no license). There is also StatSigMa, which is written in C++ and depends on muscle. However, it is beta and has no license.
Multiple alignment viewers and editors
Program |
Licence |
Packaging |
Importance |
GPL |
easy, may depend on apache |
free |
|
GPL |
depends on java |
free |
|
GPL |
depends on java |
free |
|
strap |
? |
depends on java |
|
xced |
adademic |
no sources available |
rare |
Phylogenetic analysis
Task |
Program |
Licence |
Packaging |
Importance |
Simulated evolution |
not found |
unofficial (ens-lyon) |
free |
|
Simulated evolution |
BSD |
unofficial (ens-lyon) |
free |
|
Tree inference |
GPL |
easy |
free and popular |
|
Tree inference |
BSD |
easy |
free and popular |
|
Confidence assessment |
GPL |
straightforward |
free |
|
Visualisation of reconciliations |
GPL |
depends on a patched version of the GNU plotutils |
free |
|
Tree display |
Phylodendron |
pre-release of 1996 |
java knowledge needed |
nice output |
Tree display and manipulation |
ATV |
java knowledge needed |
looks powerful |
|
Tree display |
GPL |
depends on Tcl/Tk |
looks comprehensive |
|
Coloring tree |
GPL |
perl cgi knowledge needed |
free |
|
3D Trees |
GPL |
java knowledge needed |
free, looks powerful |
|
Selecting evolution model |
GPL |
depends on java |
free |
|
Calculating rates of evolution |
no licence found |
make fails |
|
|
Detects families |
No licence found |
Depends on Perl |
|
|
Merges trees into a graph |
|
Depends on java |
|
|
Merges trees into a graph |
|
Depends on Tk |
|
Motif detection
Program |
Licence |
Packaging |
Importance |
GPL |
maybe easy |
free |
|
Artistic |
looks easy |
free |
|
LGPL |
depends on libtie-ixhash-perl, looks easy |
free |
|
no licence found |
easy |
possible alternative to MEME |
|
academic |
popular |
||
Academic |
builds fine |
Will not be packaged unless requested |
|
not found |
one .c file only! |
|
|
check with DebianLegal first |
|
||
Academic |
Sources not available |
maybe too closed |
|
not found |
Depends on Python |
|
Also, the following software is related:
Task |
Program |
Licence |
Packaging |
Importance |
Motif representation |
BSD |
perl cgi |
free |
Secondary structure of nucleic acids
Task |
Program |
Licence |
Packaging |
Importance |
display, manipulate and interconnect RNA data |
Public domain |
depends on java |
free |
|
RNA secondary structure |
BSD |
looks easy |
free |
|
prediction of structural RNAs from sequence aligments |
Depends on the Vienna RNA package |
|
||
Predicting structural motifs in aligned nucleotide sequences |
not found |
depends on java |
|
|
RNA secondary structure |
Same as Vienna package (non-free) |
Mixture of C and Java |
|
|
Prediction of secondary structure from multiple alignment |
No redistribution fee except media costs |
Depends on Haskell |
|
|
Nucleic acid folding |
looks easy |
|
Micro RNAs
Task |
Program |
Licence |
Packaging |
Importance |
Hairpin predictor |
GPL |
compiles with gcj ?HairpinPredictor.java -I ?AlgorithmQuick.* --main=?HairpinPredictor |
free |
|
miRNA target discovery |
GPL |
Depends on the Vienna package |
would be in "contrib" |
|
pre-miRNA predictor |
GPL |
Depends on python, Vienna RNA and GIST |
contrib |
|
target prediction |
BSD |
Depends on the Vienna package |
contrib |
|
Task |
Program |
Licence |
Packaging |
Importance |
Other software
Task |
Program |
Licence |
Packaging |
Importance |
Software suite |
unkonwn |
depends on pascal |
|
|
Base calling for ABI |
public domain |
looks easy |
the only free base caller for linux? |
|
Multiple alignment (graphic) |
pipmaker |
GPL |
looks easy |
free alternative to vista? |
Multiple alignment (graphic) |
vista |
academic |
downloading sources require registration |
popular |
Multiple alignment (graphic) |
mussa |
GPL |
looks easy |
free |
QA of mutiple alignments |
GPL |
easy |
free |
|
Comparative sequence analysis |
FamilyJewelsII |
LGPL or GPL, have to look in the cvs |
depends on FLTK |
free |
Parser for blast output |
GPL |
depends on perl |
useful on local installations |
|
Parser for blast output |
GPL |
C library, perl module |
says to be faste |
|
Parser for blast output |
no licence |
trivial |
Not enough for a package. Group with other scripts? |
|
Prediction of coding sequence |
GPL |
not tried |
free |
|
Masking low-complexity strings |
No licence |
trivial |
used in GCG |
|
Masking low-complexity strings |
No licence |
trivial |
advertised in FASTA |
|
Matching EST to genome |
not found |
looks simple |
an alternative, sim4, is already packaged |
|
Protein analysis |
GPL |
depends on R, blast2, java |
free |
|
Protein analysis |
Apache |
depends on java |
free |
|
Cis-elements prediction |
Not found |
various sub-components |
|
|
Semi-automated sequence analysis |
Public domain |
Depends on webbrowser, hmmer, clustalw, ncbi-toolkit, blast, and other programs |
free |
|
ORF finding |
GPL |
Depends on python |
free |
|
ORF finding |
Public domain |
optionaly depends on webserver |
free |
|
ORF finfing |
GPL |
seems simple to package |
free |
|
CpG islands prediction |
not found |
perl script, could be grouped with others |
|
|
Pretty printing of aligmnents |
non free (commercial licence is 1000 euros) |
fortran program |
not packaged unless requested |
|
Structural alignment |
Academic |
should be easy |
not packaged unless requested |
|
snoRNA discovery |
not found |
depends on Vienna and Mfold |
would be in "contrib" |
|
snoRNA discovery |
GPL |
depends on Vienna |
would be in "contrib" |
|
snoRNA discovery |
GPL |
depends on biosquid |
free |
|
snoRNA discovery |
GPL |
depends on bioperl and biosquid |
free |
|
conserved elements discovery |
looks trivial |
free |
||
graphical representation |
website says opensource |
depends on java |
free? |
|
Categorisation of Hox proteins |
CC-GPL |
depends on java |
free |
|
Classification of tRNAs |
GPL |
free |
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