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

Jemboss

GPL

part of ?pkg-emboss

free

wemboss

GPL

perl CGI?

free

Pasteur Institute Software Environment (Pise)

GPL

complex

free

SMS

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

STARS

GPL

depends on Staden

free

trev (Staden)

BSD

packaging the whole Staden seems difficlut

vital

TraceView

Not found

Depends on JAVA

Abiview has a better command line interface, and trev has a better gui.

Sequence assembly

Program

Licence

Packaging

Importance

ContigViewer

GPL

depends on python

Works on CAP3 output

DNPTrapper

BSD

depends on Qt and BerkeleyDB

specialised on finishing

Database querying

Program

Licence

Packaging

Importance

SSAHA

GPL

easy ?

popular alternative to BLAT

RaveNnA

GPL

big package

free

rsearch

GPL

Depends on squid

free

RSmatch

not found

Depends on java and recommends the Vienna package

erpin

not found

looks easy

BLAT

non-free

no

popular

fasta

academic

upstream does not want, but there is one in bio-linux

popular

SSAHA2

Academic, maybe closed source

Hopeless: depends on phrap/cross_match

unpackageable

wublast

non-free

impossible

unpackageable

Pairwise alignment

Program

Licence

Packaging

Importance

CONTRAlign

Public domain

straightforward

free

NeoBio

GPL

depends on java

free, has GUI and command line, and supports multiple algorithms

jaligner

GPL

depends on java

has a GUI

Yass

GPL

trivial

free

foldalign

GPL

should be easy

free

sim

not found

trivial

many alternatives... benchmark ?

ariadne

disclaimer

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)

CompLearn NCD

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

kalignvu

GPL

easy, may depend on apache

free

SOAP

GPL

depends on java

free

jalview

GPL

depends on java

free

strap

?

depends on java

xced

adademic

no sources available

rare

Phylogenetic analysis

Task

Program

Licence

Packaging

Importance

Simulated evolution

Treevolve

not found

unofficial (ens-lyon)

free

Simulated evolution

Seq-Gen

BSD

unofficial (ens-lyon)

free

Tree inference

MrBayes

GPL

easy

free and popular

Tree inference

QSearch

BSD

easy

free and popular

Confidence assessment

CONSEL

GPL

straightforward

free

Visualisation of reconciliations

PriMETV

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

Forester

java knowledge needed

looks powerful

Tree display

TreeDyn

GPL

depends on Tcl/Tk

looks comprehensive

Coloring tree

PhyloView

GPL

perl cgi knowledge needed

free

3D Trees

walrus

GPL

java knowledge needed

free, looks powerful

Selecting evolution model

ProtTest

GPL

depends on java

free

Calculating rates of evolution

r8s

no licence found

make fails

Detects families

BranchClust

No licence found

Depends on Perl

Merges trees into a graph

Splitstree4

Depends on java

Merges trees into a graph

Splitstree

Depends on Tk

Motif detection

Program

Licence

Packaging

Importance

PhyloGibbs

GPL

maybe easy

free

ELPH

Artistic

looks easy

free

CisPlusFinder

LGPL

depends on libtie-ixhash-perl, looks easy

free

glam

no licence found

easy

possible alternative to MEME

MEME and MAST

academic

unofficial packages

popular

MEMERIS

Academic

builds fine

Will not be packaged unless requested

MotifEnumerator

not found

one .c file only!

AlignACE

Harvard EULA

check with DebianLegal first

DME

Academic

Sources not available

maybe too closed

SLIMDisc

not found

Depends on Python

Also, the following software is related:

Task

Program

Licence

Packaging

Importance

Motif representation

weblogo/seqlogo

BSD

perl cgi

free

Secondary structure of nucleic acids

Task

Program

Licence

Packaging

Importance

display, manipulate and interconnect RNA data

S2S

Public domain

depends on java

free

RNA secondary structure

CONTRAfold

BSD

looks easy

free

prediction of structural RNAs from sequence aligments

RNAz

Academic

Depends on the Vienna RNA package

Predicting structural motifs in aligned nucleotide sequences

ddbRNA

not found

depends on java

RNA secondary structure

RNAshapes

Same as Vienna package (non-free)

Mixture of C and Java

Prediction of secondary structure from multiple alignment

RNAlishape

No redistribution fee except media costs

Depends on Haskell

Nucleic acid folding

UNAfold

academic

looks easy

Micro RNAs

Task

Program

Licence

Packaging

Importance

Hairpin predictor

ScorePin

GPL

compiles with gcj ?HairpinPredictor.java -I ?AlgorithmQuick.* --main=?HairpinPredictor

free

miRNA target discovery

miRanda

GPL

Depends on the Vienna package

would be in "contrib"

pre-miRNA predictor

miRNA SVM

GPL

Depends on python, Vienna RNA and GIST

contrib

target prediction

MicroTar

BSD

Depends on the Vienna package

contrib

Task

Program

Licence

Packaging

Importance

Other software

Task

Program

Licence

Packaging

Importance

Software suite

delila

unkonwn

depends on pascal

Base calling for ABI

autoseq

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

mumsa

GPL

easy

free

Comparative sequence analysis

FamilyJewelsII

LGPL or GPL, have to look in the cvs

depends on FLTK

free

Parser for blast output

html4blast

GPL

depends on perl

useful on local installations

Parser for blast output

zerg

GPL

C library, perl module

says to be faste

Parser for blast output

blast2html

no licence

trivial

Not enough for a package. Group with other scripts?

Prediction of coding sequence

Critica

GPL

not tried

free

Masking low-complexity strings

xnu

No licence

trivial

used in GCG

Masking low-complexity strings

pseg

No licence

trivial

advertised in FASTA

Matching EST to genome

est_genome

not found

looks simple

an alternative, sim4, is already packaged

Protein analysis

prompt

GPL

depends on R, blast2, java

free

Protein analysis

Amino Acid Explorer

Apache

depends on java

free

Cis-elements prediction

poxo

Not found

various sub-components

Semi-automated sequence analysis

SEALS

Public domain

Depends on webbrowser, hmmer, clustalw, ncbi-toolkit, blast, and other programs

free

ORF finding

Virtual Ribosome

GPL

Depends on python

free

ORF finding

orfind

Public domain

optionaly depends on webserver

free

ORF finfing

geneid

GPL

seems simple to package

free

CpG islands prediction

CpGcluster

not found

perl script, could be grouped with others

Pretty printing of aligmnents

ESPript

non free (commercial licence is 1000 euros)

fortran program

not packaged unless requested

Structural alignment

CE

Academic

should be easy

not packaged unless requested

snoRNA discovery

snoSeeker

not found

depends on Vienna and Mfold

would be in "contrib"

snoRNA discovery

snoReport

GPL

depends on Vienna

would be in "contrib"

snoRNA discovery

snoScan

GPL

depends on biosquid

free

snoRNA discovery

snoGPS

GPL

depends on bioperl and biosquid

free

conserved elements discovery

FastCompare

free

looks trivial

free

graphical representation

graphDNA

website says opensource

depends on java

free?

Categorisation of Hox proteins

HoxPred

CC-GPL

depends on java

free

Classification of tRNAs

TFAM

GPL

Depends on ?BioPerl and coveaf

free


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