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Comment: Clustering section taken over to tasks file
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amos is on tasks page
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||Assembling||[[http://amos.sourceforge.net/|amos]]||Artistic||depends on Perl and Qt||free|| |
Short explanation:
This page lists programs which are usefull to the field of Genomics. It is mostly software related to microarrays, genome sequencing, and whole-genome analysis.
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!.
Unsorted
Task |
Program |
Licence |
Packaging |
Importance |
RNA mapping |
no profit, no redistribution of modified versions |
impossible? |
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Comparatige genomics |
Prior agreement required |
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Genome Browser |
GPL |
depends on java |
flash plugin required for use |
|
Database schema |
not found |
xml schema |
|
|
Generic database framework |
BSD |
depends on java and perl |
Used by many databases |
|
Manipulating gff files |
no licence |
lot of manpages to write! |
|
|
Multiple alignments |
academic |
would depend on clustalw and fastdnaml |
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EST clustering |
not found |
Haskell program, did not build on ppc |
|
|
Discovery of regulatory regions |
GPL |
depends on python |
free |
|
genomic sequence analysis tools |
GPL+LGPL |
doesn't seem difficult |
|
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Genetic maps |
no licence |
php cgi |
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Database of SAGE tags |
not found |
perl and sh scripts |
|
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Visualisation of annotations |
Not found |
Depends on gtk, xml, dbi, bioperl, ... |
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SNP analysis |
GPL |
C program plus website |
free |
|
Gene predicion |
Not found |
./configure && make fails, but it seems easy to fix |
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Rearrangements analysis |
GPL |
straightforward |
free |
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Inversion and rearrangement location |
|
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Database clustering |
Not found, but homepage says open source |
Straighytforward |
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cis-regulatory element analysis |
MIT |
depends on python and sqlite |
free |
|
Gel analysis |
Depends on java |
Will not be packaged unless requested |
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Gene structure annotation and analysis |
Artistic |
C++, Perl |
|
|
Annotation |
LGPL |
depends on Java |
free |
|
Gene finding in prokaryotes |
GPL |
Depends on bioperl, python, hmmer, and libsvm |
free, complex dependancies |
|
Analysis of high-throughput data |
Artistic |
Depends on Java and Perl |
free |
|
Task |
Program |
Licence |
Packaging |
Importance |
Microarrays
Task |
Program |
Licence |
Packaging |
Importance |
Suite |
artistic |
depends on java |
free |
|
Suite |
GNU and Affero GPL |
Depends on webserver, R, and python |
free |
|
Microarrays |
GPL |
depends on R |
free |
|
Microarrays |
GPL |
R package depending on bioconductor |
free |
|
Image analysis for microarrays |
GPL |
depends on Qt, FFTW |
free |
|
Clustering |
GPL |
depends on QT4 |
free |
|
Microarrays |
not found |
looks easy |
|
|
Normalisation |
GPL |
R module depending on Bioconductor |
free |
|
Genome-scale oligonucleotide design |
GPL |
Depends on Java |
free |
|
Comparison between experiments |
GPL |
Depends on perl |
free |
|
False Discovery Rate |
not found |
R library |
|
|
False Discovery Rate |
LGPL |
R library |
free |
|
Combining Batches |
Not found |
R script |
|
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Submission to ?ArrayExpress |
Apache |
Depends on Perl. Would provide libarrayexpress-perl? |
free |
|
Submission to MIAMExpress |
Contains an acknowledgement clause |
Depends on Apache, Perl-CGI and MySQL |
maybe non-DFSG-free |
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FDR evaluation |
LGPL |
depends on R and Tk |
free |
|
Task |
Program |
Licence |
Packaging |
Importance |
Repeats
Task |
Program |
Licence |
Packaging |
Importance |
Repeat finding |
GPL |
looks easy |
free |
|
Repeat finding |
Public domain |
looks easy |
free |
|
Repeat masking |
Not found |
|
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Repeats analysis |
Not found |
straightforward |
|
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Repeat finding |
Not found |
straightforward |
|
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Repeat finding |
not found |
Depends on java and pngencoder (LGPL) |
|
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Finding ?RepBase repeats in sequences |
not found |
Maybe depends on wu-blast |
contains a standalone blast parser |
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Repeat masking |
Open Software License v. 2.1 |
depends on perl |
Not sure if it is DFSG-free? |
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Task |
Program |
Licence |
Packaging |
Importance |
Genome assembling
Task |
Program |
Licence |
Packaging |
Importance |
Assembling |
OSI-certified |
|
free |
|
Assembling |
commercial product open only to registered academics |
depends on Perl |
not redistributable |
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Assembling |
|
non-free |
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Assembling |
depends on phrap |
non-free |
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BAC scaffolding |
GPL |
trivial |
free |
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BAC scaffolding |
Academic |
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Base calling |
BSD with advertising clause |
Does not compile out of the box |
|
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Base calling |
Public domain |
Old C++ which may not be compatible with recent gcc |
free |
|
Band calling |
unknown |
did not find the sources |
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