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

GMAP

no profit, no redistribution of modified versions

impossible?

Comparatige genomics

BSR

non-free

Prior agreement required

Genome Browser

OmicBrowser

GPL

depends on java

flash plugin required for use

Database schema

FuGE

not found

xml schema

Generic database framework

GUS

BSD

depends on java and perl

Used by many databases

Manipulating gff files

gffTools

no licence

lot of manpages to write!

Multiple alignments

MAVID

academic

would depend on clustalw and fastdnaml

EST clustering

xsact

not found

Haskell program, did not build on ppc

Discovery of regulatory regions

Enhancer Element Locator

GPL

depends on python

free

genomic sequence analysis tools

Cartwheel Bioinformatics Package

GPL+LGPL

doesn't seem difficult

Genetic maps

MapMerger

no licence

php cgi

Database of SAGE tags

identitag

not found

perl and sh scripts

Visualisation of annotations

MuGeN

Not found

Depends on gtk, xml, dbi, bioperl, ...

SNP analysis

QualitySNP

GPL

C program plus website

free

Gene predicion

Diogenes

Not found

./configure && make fails, but it seems easy to fix

Rearrangements analysis

Grappa

GPL

straightforward

free

Inversion and rearrangement location

GRIL

non-free

Database clustering

CD-HIT

Not found, but homepage says open source

Straighytforward

cis-regulatory element analysis

cistematic

MIT

depends on python and sqlite

free

Gel analysis

GelBuddy

Academic with invariant sections

Depends on java

Will not be packaged unless requested

Gene structure annotation and analysis

PASA

Artistic

C++, Perl

Annotation

Genepi

LGPL

depends on Java

free

Gene finding in prokaryotes

gismo

GPL

Depends on bioperl, python, hmmer, and libsvm

free, complex dependancies

Analysis of high-throughput data

APED

Artistic

Depends on Java and Perl

free

Task

Program

Licence

Packaging

Importance

Microarrays

Task

Program

Licence

Packaging

Importance

Suite

TM4

artistic

depends on java

free

Suite

asterias

GNU and Affero GPL

Depends on webserver, R, and python

free

Microarrays

SNOMAD

GPL

depends on R

free

Microarrays

amda

GPL

R package depending on bioconductor

free

Image analysis for microarrays

Dapple

GPL

depends on Qt, FFTW

free

Clustering

gedas

GPL

depends on QT4

free

Microarrays

Vera, Sam

not found

looks easy

Normalisation

Goulphar

GPL

R module depending on Bioconductor

free

Genome-scale oligonucleotide design

OligoArray 2.1

GPL

Depends on Java

free

Comparison between experiments

L2L

GPL

Depends on perl

free

False Discovery Rate

FDRlibrary

not found

R library

False Discovery Rate

samr

LGPL

R library

free

Combining Batches

ComBat

Not found

R script

Submission to ?ArrayExpress

tab2MAGE

Apache

Depends on Perl. Would provide libarrayexpress-perl?

free

Submission to MIAMExpress

miamexpress

Contains an acknowledgement clause

Depends on Apache, Perl-CGI and MySQL

maybe non-DFSG-free

FDR evaluation

QVALUE

LGPL

depends on R and Tk

free

Task

Program

Licence

Packaging

Importance

Repeats

Task

Program

Licence

Packaging

Importance

Repeat finding

TPRpred

GPL

looks easy

free

Repeat finding

PILER

Public domain

looks easy

free

Repeat masking

RBR

Not found

unfficial

Repeats analysis

RepeatGluer

Not found

straightforward

Repeat finding

RepeatScout

Not found

straightforward

Repeat finding

TRUST

not found

Depends on java and pngencoder (LGPL)

Finding ?RepBase repeats in sequences

censor

not found

Maybe depends on wu-blast

contains a standalone blast parser

Repeat masking

RepeatMasker

Open Software License v. 2.1

depends on perl

Not sure if it is DFSG-free?

Task

Program

Licence

Packaging

Importance

Genome assembling

Task

Program

Licence

Packaging

Importance

Assembling

phrap

commercial product open only to registered academics

depends on Perl

not redistributable

Assembling

Arachne

Academic

non-free

Assembling

Atlas

Academic

depends on phrap

non-free

BAC scaffolding

FASSI

GPL

trivial

free

BAC scaffolding

fpc

Academic

Base calling

bass

BSD with advertising clause

Does not compile out of the box

Base calling

autoseq

Public domain

Old C++ which may not be compatible with recent gcc

free

Band calling

Image

unknown

did not find the sources


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