Task: Biology
Install: true
Description: Debian Med bioinformatics packages
 This metapackage will install Debian packages for use in molecular biology,
 structural biology and other biological sciences.

X-Begin-Category: Phylogenetic analysis

Recommends: altree

Recommends: beast-mcmc, beast2-mcmc

Recommends: fastdnaml, njplot, tree-puzzle | tree-ppuzzle

Recommends: probalign

Recommends: treeviewx

Recommends: figtree

Recommends: hyphy-mpi | hyphy-pt

Recommends: spread-phy

Recommends: omegamap
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Recommends: sweed

X-End-Category: Phylogenetic analysis

Recommends:     phylip
Why:         Phylogenetic analysis (Non-free, thus only suggested).

X-Comment: treetool is removed from Debian because it is not maintained upstream since
 1995 and cause the Xserver to freeze under Squeeze

Recommends:     fastlink, loki, plink, plink1.9, plink2, r-cran-qtl, r-cran-genabel, gemma, bolt-lmm
Why:         Genetics

X-Begin-Category: Sequence alignments and related programs.

Recommends:     amap-align
Remark: Dead upstream
 The homepage of this project vanished as well as the Download area.  An
 old unmaintained version remained at code.google.com.  Please drop the
 maintainer a note if you have any news of this project.
 
Suggests: conda-package-handling

Recommends:     boxshade, gff2aplot, muscle, muscle3, sim4, sibsim4, tabix, wise

Recommends: maqview

Recommends: blasr

Recommends: daligner

Suggests: dascrubber

Recommends: mhap

Recommends: bwa

Recommends: megahit

Recommends: metabat

Recommends: mummer, e-mem

Recommends: ncbi-blast+-legacy, plast

Recommends: ncbi-blast+

Recommends: mafft

Recommends: sra-toolkit

Recommends: t-coffee

Recommends: kalign

Recommends: ghmm, hmmer

Recommends: gramalign

Recommends: exonerate

Recommends: elph

Recommends: dialign

Recommends: dialign-tx

Recommends: poa

Recommends: probcons

Recommends: proda

Recommends: seaview

Recommends: sigma-align

Recommends: wham-align

Recommends: emboss

Recommends: embassy-domalign, embassy-domainatrix, embassy-domsearch, embassy-phylip
Suggests:    emboss-explorer
Why:         The EMBOSS sequence analysis suite and its galaxy.

Recommends:     arb
Why:         Sequence alignments and related programs (Non-free, thus only suggested).

Recommends: clustalx, clustalo

Recommends: clustalw

Recommends: mothur, bowtie, bowtie2

Recommends: transtermhp

X-End-Category: Sequence alignments and related programs.

X-Begin-Category: high-throughput sequencing

Recommends: bustools

Suggests: dnapi

Recommends: last-align, maq, ssake, velvet | velvet-long

Recommends: qiime

Suggests: nano-snakemake

Suggests: catfishq

Suggests: q2-cutadapt,
          q2-demux,
          q2-feature-classifier,
          q2-feature-table,
          q2-metadata,
          q2-quality-filter,
          q2-types,
          q2cli,
          q2templates

Suggests: q2-taxa,
         q2-alignment,
         q2-emperor,
         q2-composition,
         q2-sample-classifier,
         q2-vsearch,
         q2-dada2,
         q2-deblur,
         q2-diversity,
         q2-gneiss,
         q2-longitudinal,
         q2-phylogeny,
         q2-quality-control,
         q2-fragment-insertion

Recommends: scoary

Suggests: tandem-genotypes

Recommends: tophat,
            tophat-recondition

Recommends: umap

Recommends: python3-bioxtasraw

Suggests: python3-intake

Suggests: python3-ncls

Suggests: python3-pychopper

Suggests: python3-pyrle

Suggests: python3-pyranges

X-End-Category: high-throughput sequencing

X-Begin-Category: Analysis of RNA sequences.

Recommends: infernal

Recommends: rnahybrid

Suggests: python3-anndata

X-End-Category: Analysis of RNA sequences.

X-Begin-Category: Molecular modelling and molecular dynamics

Recommends:     adun-core

Suggests:    adun.app

Recommends:     avogadro, garlic, gamgi, gdpc, ghemical, jmol, pymol, r-cran-bio3d, massxpert, minexpert2

Recommends: gromacs

Suggests: illustrate

Recommends: rasmol, viewmol, qutemol

Recommends: modeller
Pkg-URL: http://salilab.org/modeller/release.html#deb
Remark: The package is created independently from Debian Med or Debian Science.
 The source code
 is not generally available. Hence, most users are limited to the compiled
 versions of MODELLER. The program is distributed as a single install file
 that contains scripts, libraries, examples, documentation (in PDF and
 HTML formats) and executables for the supported platforms and operating
 systems. Please refer to the relevant section below for your platform:
 .
 The program comes as closed source, only free for academia,
 see http://salilab.org/modeller/registration.html.

X-End-Category: Molecular modelling and molecular dynamics

Recommends:     plasmidomics
Why:         Presentation

X-Begin-Category: Tools for the molecular biologist.

Recommends:     gff2ps, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, readseq, tigr-glimmer

Recommends: melting

Recommends: mipe

Recommends: primer3

X-End-Category: Tools for the molecular biologist.

X-Begin-Category: Genome Browser

Recommends: artemis

Recommends: gbrowse
X-Importance: Academic ones are really expensive for commercial use

X-End-Category: Genome Browser

Recommends: python3-biomaj3-daemon

Ignore: mozilla-biofox
Remark: biofox was removed from Debian (see #727689)
 The bug log (http://bugs.debian.org/727689) explains the reasons for
 the removal.  Please keep us informed if you become aware about
 upstream changes that enable using this plugin for firefox >= 10.

Recommends:     glam2
Why:         Motif search

Recommends: raster3d

Recommends: phyml

Recommends: autodock
Why:         Molecular modelling and molecular dynamics.

Recommends: autogrid

Recommends: autodock-vina

Recommends: mustang

Recommends: probabel

Recommends: theseus

Recommends: staden-io-lib-utils

Recommends: samtools, bedtools, datamash

#Recommends: gassst
# Removed in bug #689957

Recommends: hinge

Recommends: seq-gen

Recommends: snp-sites

Recommends: mira-assembler

Recommends: alien-hunter

Recommends: seqan-apps, seqan-needle, seqan-raptor

Recommends: ncoils

Recommends: gentle

Recommends: gmap

Recommends: igv

Recommends: r-other-rajewsky-dropbead

Recommends: picard-tools

Recommends: acedb-other

Recommends: blixem, dotter, belvu

Recommends: paml

Recommends: velvetoptimiser

Recommends: ensembl
Pkg-URL: http://snapshot.debian.org/package/ensembl/63-1/
Remark: Ensembl was removed from Debian due #645487
 Ensembl used to be in Debian experimental branch but was removed for formal reasons which
 are explained in http://bugs.debian.org/645487

Recommends: mrbayes

Recommends: pdb2pqr

Recommends: clonalframe, clonalframeml

Recommends: dssp

Recommends: jellyfish, jellyfish1

Recommends: ballview

Recommends: pizzly

Recommends: raxml

Recommends: mlv-smile

Recommends: cd-hit

Recommends: cufflinks

Recommends: eigensoft

Recommends: grinder

Recommends: jalview

Recommends: reprof

Recommends: tm-align

Recommends: norsnet

Recommends: norsp

Recommends: predictnls

Recommends: prime-phylo

Recommends: proftmb

Recommends: profbval

Recommends: profisis

Recommends: hhsuite

Recommends: ffindex

Recommends: flexbar

Recommends: blimps-utils

Recommends: sift

Recommends: neobio

Recommends: ray

Recommends: ugene

Recommends: soapdenovo, soapdenovo2, soapsnp, soapaligner

Recommends: microbiomeutil, chimeraslayer, nast-ier, wigeon

Recommends: minia

Recommends: trimmomatic, trim-galore

Recommends: saint

Recommends: rtax

Recommends: rate4site

Recommends: rna-star

Recommends: sailfish

Recommends: topp, openms

Recommends: scythe

Recommends: sickle

Recommends: skewer

Recommends: kmc

Recommends: king-probe

Recommends: ncl-tools

Recommends: tvc

Suggests: science-workflow

Recommends: libvcflib-tools

Recommends: bppsuite, bppphyview

Recommends: bioawk

Suggests: getdata

X-Mark: Prospective packages are starting here

X-Mark: Packages in Vcs - Information about these is queried from UDD as well

Recommends: acacia

Recommends: adapterremoval

Recommends: aegean

Recommends: andi

Recommends: any2fasta

Recommends: arden

Recommends: artfastqgenerator, art-nextgen-simulation-tools

Recommends: assemblytics

Recommends: ataqv

Recommends: augustus

Recommends: baitfisher

Recommends: bandage

Recommends: bbmap

Recommends: bcalm

Recommends: beagle

Recommends: bedops

Recommends: biceps
Remark: Mentioned at http://www.renard.it/, developed in RKI

Recommends: bio-vcf

Recommends: btllib-tools

Recommends: cnvkit

Recommends: csb

Recommends: diamond-aligner

Recommends: python3-emperor

Recommends: euler2, euler-sr

Recommends: fitgcp

Recommends: gasic

Recommends: ipig

Recommends: abpoa

Recommends: aevol

Recommends: agat

Recommends: alter-sequence-alignment

Recommends: amos-assembler, hawkeye
Language: Perl

Recommends: anfo

Recommends: apollo

Recommends: aragorn

Recommends: ariba

Recommends: arvados

Recommends: assembly-stats

Recommends: atac

Recommends: atropos

Recommends: augur

Recommends: axe-demultiplexer

Recommends: axparafit, axpcoords

Recommends: bali-phy

Recommends: bamclipper

Recommends: bamkit

Recommends: bamtools

Recommends: bagpipe

Recommends: barrnap

Recommends: bax2bam

Recommends: bcbio

Recommends: bcftools

Recommends: bigsdb

Recommends: bio-eagle

Recommends: bio-tradis

Recommends: biobambam2

Recommends: biosyntax

Recommends: bismark

Recommends: bifrost

Recommends: bitseq

Recommends: blat

Recommends: blobology

Recommends: bio-rainbow

Recommends: braker

Recommends: busco

Recommends: card-rgi

Recommends: cassiopee

Recommends: cat-bat

# Recommends: ccs
# Removed https://tracker.debian.org/news/592502/ccs-removed-from-testing/

Recommends: cdbfasta

Recommends: centrifuge

Recommends: cellprofiler

Recommends: chromhmm

Recommends: cgview, brig, cct

Recommends: cif-tools

Recommends: cinema
Language: Java

Recommends: circlator

Recommends: clearcut

Recommends: clonalorigin

Recommends: cluster3

Recommends: chromimpute

Recommends: codonw

Recommends: comet-ms

Recommends: condetri

Recommends: contrafold

Recommends: covpipe

Recommends: covtobed

Recommends: crac

Recommends: crossbow
X-Category: Sequencing

Recommends: crux-toolkit

Recommends: ctffind

Recommends: cutadapt

Recommends: cutesv

Recommends: cytoscape

Recommends: damapper

Recommends: dawg

Recommends: dazzdb

Recommends: dazzle

Recommends: deepbinner

Recommends: density-fitness

Recommends: dextractor

Recommends: delly

Recommends: deepnano
Remark: There is no intend to keep continue the existing packaging since
 the program nanocall seems to serve the intended purpose better

Recommends: dendroscope

Recommends: deblur

Recommends: diann

Recommends: dnarrange

Recommends: drop-seq-tools

Recommends: dwgsim

Recommends: ea-utils

Recommends: ecell

Recommends: ecopcr

Recommends: edtsurf

Recommends: emmax

Recommends: ensembl-vep

Recommends: examl, raxml-ng

Recommends: exabayes

Recommends: berkeley-express

Recommends: fasta3

Recommends: fastani

Recommends: fasttree, veryfasttree

Recommends: fastahack

Recommends: fastaq

Recommends: fastml

Recommends: fastp

Recommends: fastq-pair

Recommends: fastqc

Recommends: fastqtl

Recommends: flappie

Recommends: flash

Recommends: flye

Recommends: ffp

Recommends: fieldbioinformatics

Recommends: filtlong

Recommends: unc-fish

Recommends: fml-asm

Recommends: forester
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-amd64
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
 BioLinux was following the upstream name change to archaeopteryx and thus the
 package is called bio-linux-archaeopteryx there.
 .
 The binary package is full of JARs without source.

Recommends: freecontact

Recommends: freebayes

Recommends: fsa
Enhances: t-coffee
Remark: Precondition for T-Coffee
 see http://wiki.debian.org/DebianMed/TCoffee
 .
 Upstream address bounced when contacting about segfaults so it seems to be
 dead upstream and no good code quality.

Recommends: fsm-lite

Recommends: garli

Recommends: gatb-core

Recommends: gatk

Recommends: genometester

Recommends: genomethreader

Recommends: genometools

Recommends: genomicsdb-tools

Recommends: gerp++

Recommends: gffread

Recommends: ggd-utils

Recommends: grabix

Recommends: graphbin

Recommends: graphlan

Recommends: graphmap2

Recommends: gsort

Recommends: gwama

Recommends: gubbins

Recommends: haploview

Recommends: harvest-tools

Recommends: hilive

Recommends: hisat2

Recommends: hmmer2
Remark: This older version of HMMER is used in some applications
 While Debian has HMMER 3 since some time there are users of
 HMMER 2 interested in having this old version available and
 thus the package is reintroduced.

Recommends: htqc

Suggests: hts-nim-tools

Recommends: idba

Recommends: idefix

Suggests: idseq-bench

Recommends: indelible

Recommends: insilicoseq

Recommends: iqtree

Recommends: iva

Recommends: jaligner

Recommends: jbrowse

Recommends: jmodeltest

Recommends: kallisto

Recommends: kaptive, kleborate

Recommends: kempbasu

Recommends: khmer

Recommends: kmer

Recommends: kineticstools

Recommends: kissplice

Recommends: kma

Recommends: kmerresistance

Recommends: kraken, kraken2

Recommends: lagan
X-Category: Comparative genomics

Recommends: lamassemble

Recommends: lambda-align, lambda-align2

Recommends: lastz

Recommends: leaff

Suggests: libhdf5-dev

Suggests: libhnswlib-dev

Recommends: ltrsift

Recommends: lofreq


Recommends: radiant

Recommends: lefse

Recommends: libpwiz-tools

Recommends: lighter

Recommends: lumpy-sv

Recommends: mach-haplotyper

Recommends: macs

Recommends: macsyfinder

Recommends: maffilter

Recommends: mage2tab, tab2mage

Recommends: malt

Recommends: manta

Recommends: mapdamage

Recommends: marginphase

Recommends: martj

Recommends: mash

Recommends: progressivemauve
X-Category: Multiple genome alignment
X-Importance: efficient

Recommends: mauve-aligner

Recommends: mcaller

Recommends: mecat2

Recommends: medaka

Recommends: megan-ce

Recommends: meme
License: non-free for commercial purpose (http://meme.nbcr.net/meme/COPYRIGHT.html)

Recommends: meryl

Recommends: metabit

Recommends: metaphlan

Recommends: metastudent

Suggests: metastudent-data, metastudent-data-2

Recommends: metaeuk

Recommends: microbegps

Recommends: mindthegap

Recommends: miniasm

Recommends: minimac4

Recommends: minimap, minimap2

Recommends: mirtop

Recommends: mmb

Recommends: molekel

Recommends: mosaik-aligner

Recommends: mosdepth

Recommends: mmseqs2

Recommends: mpsqed

Suggests: mrs
Remark: mrs might occupy a lot of space on users disk - so you want to avoid this package from the metapackage recommends

Recommends: mptp

Recommends: mugsy

Recommends: multiqc

Recommends: murasaki | murasaki-mpi

Recommends: mview

Recommends: nanocall

Suggests: nanocomp

Recommends: nanofilt

# Suggests: nanoget - see python3-nanoget

Recommends: nanolyse

# Suggests: nanomath - see python3-nanomath

Recommends: nanook

Recommends: nanoplot

Recommends: nanopolish

Recommends: nanostat

Recommends: nanosv

Recommends: ncbi-acc-download

Recommends: ncbi-entrez-direct

Recommends: ncbi-magicblast

Recommends: ncbi-seg

Recommends: nextsv

Recommends: ngila

Recommends: ngmlr

Recommends: ngsqctoolkit

Recommends: ntcard

Recommends: nw-align

Recommends: nxtrim

Recommends: oases

Recommends: obitools

Recommends: oncofuse

Recommends: optimir

Recommends: optitype

Recommends: paipline

Recommends: pal2nal

Recommends: paleomix

Recommends: pangolin

Recommends: paraclu

Recommends: parasail

Recommends: parsinsert

Recommends: parsnp

Recommends: partitionfinder

Recommends: patman

Recommends: patristic
Language: Java

Recommends: pbdagcon

Recommends: pbsuite

Recommends: pbjelly, pbhoney

Recommends: pbsim

Recommends: pcma
Remark: Precondition for T-Coffee
 see http://wiki.debian.org/DebianMed/TCoffee
 .
 Check with authors about licensing, they adopted code from clustalw which is now
 free.  Thus a change might be possible

Recommends: perm

Recommends: pftools

Recommends: phast

Recommends: phipack

Recommends: phybin

Recommends: phylonium

Recommends: phylophlan
Remark: usearch can not be replaced since vsearch does not work with proteins
 See https://lists.debian.org/debian-med/2016/05/msg00091.html

Recommends: phyloviz-core
Remark: There are several plugins to package
 The download page http://www.phyloviz.net/wiki/plugins/ lists several plugins
 that should be packaged (single or as bundle) as well.

Recommends: phyutility

Recommends: phyx

Recommends: physamp

Recommends: picopore

Recommends: piler

Recommends: pilercr

Recommends: pilon

Recommends: pinfish

Recommends: pipasic, inspect, tide

Recommends: pique

Recommends: pirs

Recommends: placnet

Recommends: plasmidid

Recommends: plasmidseeker

Recommends: plato

Recommends: plip

Recommends: pomoxis

Recommends: poretools

Recommends: porechop

Recommends: pplacer

Recommends: prank

Recommends: prinseq-lite

Recommends: proalign

Recommends: prodigal

Recommends: prokka

Recommends: proteinortho

Recommends: prottest

Recommends: provean

Recommends: psortb

Recommends: pscan-tfbs, pscan-chip

Recommends: psipred

Recommends: pssh2

Recommends: pufferfish

Recommends: pullseq

Recommends: pycorrfit

Recommends: pyensembl

Recommends: pyfastx

Recommends: pyscanfcs

Suggests: python3-alignlib

Recommends: python3-cogent3

Suggests: python3-cgecore 

Suggests: python3-cyvcf2 

Suggests: python3-deeptools, python3-deeptoolsintervals

Recommends: python3-geneimpacts

Recommends: python3-gffutils

Suggests: python3-htseq

Suggests: python3-loompy

Suggests: python3-nanomath

Suggests: python3-nanoget

Recommends: python3-pairtools

Recommends: python3-pybedtools

Suggests: python3-pybel

Suggests: python3-pyfaidx 

Suggests: python3-pyflow

Suggests: python3-py2bit

Suggests: python3-pysam

Recommends: python3-sqt

Recommends: qtlreaper

Suggests: python3-tinyalign

Recommends: python3-treetime

Recommends: purple

Recommends: pycoqc

Recommends: qcat

Recommends: qcumber

Recommends: quicktree

Recommends: qtltools

Recommends: qualimap

Recommends: quast

Recommends: quorum

Recommends: ragout

Recommends: rambo-k

Recommends: rapmap

Recommends: r-bioc-annotate

Suggests: r-bioc-annotationhub

Suggests: r-bioc-aroma.light

Suggests: r-bioc-beachmat

Suggests: r-bioc-biocneighbors

Suggests: r-bioc-biocsingular

Recommends: r-bioc-biostrings

Recommends: r-bioc-bitseq

Recommends: r-bioc-cner

Suggests: r-bioc-ctc

Recommends: r-bioc-cummerbund

Suggests: r-bioc-dnacopy

Recommends: r-bioc-deseq2

Recommends: r-bioc-edger

Suggests: r-bioc-ensembldb,

Suggests: r-bioc-experimenthub

Recommends: r-bioc-genefilter

Suggests: r-bioc-geneplotter

Suggests: r-bioc-genomicalignments

Suggests: r-bioc-genomicfiles

Suggests: r-bioc-genomicranges

Recommends: r-bioc-geoquery

Suggests: r-bioc-go.db

Suggests: r-bioc-grohmm

Suggests: r-bioc-gviz

Recommends: r-bioc-hilbertvis
Remark: It would be interesting to package HilbertVisGUI as well.

Recommends: r-bioc-htsfilter

Recommends: r-bioc-impute

Suggests: r-bioc-isoformswitchanalyzer

Recommends: r-bioc-limma

Recommends: r-bioc-megadepth

Recommends: r-bioc-mergeomics

Recommends: r-bioc-metagenomeseq, r-bioc-phyloseq

Suggess: r-bioc-mfuzz

Recommends: r-bioc-mofa, r-bioc-mofa2

Recommends: r-bioc-multiassayexperiment

Recommends: r-bioc-mutationalpatterns

Suggests: r-bioc-org.hs.eg.db, r-bioc-org.mm.eg.db

# No metadata for these packages
#, r-bioc-org.rn.eg.db, r-bioc-org.ce.eg.db

Recommends: r-bioc-pcamethods

Suggests: r-bioc-qusage

Recommends: r-bioc-rtracklayer

Suggests: r-bioc-savr

Recommends: r-bioc-scater

Suggests: r-bioc-singlecellexperiment

Suggests: r-bioc-structuralvariantannotation

Recommends: r-bioc-tfbstools

Suggests: r-bioc-tximport

Recommends: r-cran-adegenet, r-cran-adephylo

Suggests: r-cran-amap

Recommends: r-cran-ape

Suggests: r-cran-biwt

Suggests: r-cran-boolnet

Suggests: r-cran-corrplot

Suggests: r-cran-dynamictreecut

Recommends: r-bioc-ebseq

Suggests: r-cran-epir 

Suggests: r-cran-fitdistrplus

Suggests: r-cran-forecast

Suggests: r-cran-gprofiler2

Suggests: r-cran-qqman

Recommends: r-cran-rotl

Suggests: r-cran-rentrez

Recommends: r-cran-samr

Recommends: r-cran-distory

Recommends: r-cran-drinsight

Recommends: r-cran-kaos

Suggests: r-cran-minerva

Suggests: r-cran-optimalcutpoints

Suggests: r-cran-parmigene

Recommends: r-cran-phangorn

Suggests: r-cran-pheatmap

Recommends: r-cran-phytools

Recommends: r-cran-pscbs

Suggests: r-cran-rcpphnsw

Suggests: r-cran-sctransform

Recommends: r-cran-seurat

Recommends: r-cran-seqinr

Recommends: r-cran-spp

Recommends: r-cran-treespace

Recommends: r-cran-tsne

Recommends: r-cran-vegan

Recommends: r-cran-webgestaltr

Recommends: r-other-apmswapp

Recommends: r-cran-spp

Recommends: r-cran-wgcna

Recommends: r-other-ascat

Recommends: r-other-fastbaps

Recommends: r-other-mott-happy.hbrem

Recommends: readucks

Recommends: recan

Recommends: relion, relion-gui, relion-cuda, relion-gui-cuda

Recommends: rdp-alignment, rdp-readseq, rdp-classifier

Recommends: reapr

Recommends: repeatmasker-recon

Recommends: repeatmasker

Recommends: resfinder

Suggests: resfinder-db

Recommends: roadtrips

Recommends: roary

Recommends: rockhopper

Recommends: roguenarok

Recommends: rosa

Recommends: rsat

Recommends: rsem

Recommends: sambamba

Recommends: samblaster

Recommends: salmid

Recommends: salmon

Recommends: samclip

Recommends: sap
Remark: Precondition for T-Coffee
 see http://wiki.debian.org/DebianMed/TCoffee

Recommends: savvy-util

Recommends: scrappie

Recommends: scrm

Recommends: seer

Recommends: segemehl

Recommends: sepp, tipp

Recommends: seq-seq-pan
Remark: Needs blat which is not re-distributable

Recommends: seqkit

Recommends: seqmagick

Recommends: seqprep

Recommends: seqsero

Recommends: seqtk

Recommends: seqwish

Suggests: seqcluster

Recommends: sga

Recommends: shasta

Recommends: shovill

Recommends: signalalign

Recommends: sibelia

Recommends: simka, simkamin

Recommends: sina

Recommends: sistr

Recommends: situs

Recommends: sim4db

Recommends: ska

Recommends: skesa

Recommends: smalt
Remark: This can be regarded as successor of ssaha2
 This program is from the same author as ssaha2 and according to its author
 faster and more precise than ssaha2 (except for sequences > 2000bp).

Recommends: smithwaterman

Recommends: smrtanalysis

Recommends: snpeff, snpsift

Recommends: snpomatic

Recommends: solvate

Recommends: sortmerna

Recommends: snap-aligner

Recommends: sniffles

Recommends: snippy

Recommends: sourmash

Recommends: spaced

Recommends: spades

Recommends: spaln

Recommends: sparta

Recommends: sprai

Recommends: srst2

Recommends: ssaha
Remark: Successor for ssaha2 available: smalt
 The program smalt is from the same author is according to its author
 faster and more precise than ssaha2 (except for sequences > 2000bp)

Recommends: sspace

Recommends: ssw-align

Recommends: staden

Recommends: stacks

Recommends: strap, strap-base
Language: Java

Recommends: strelka

Recommends: stringtie

Recommends: subread

Recommends: suitename

Recommends: sumatra, sumaclust

Recommends: sumtrees

Recommends: surankco

Recommends: surpyvor

Recommends: survivor

Recommends: svim

Recommends: swarm

Recommends: tacg
X-Category: Motif detection
X-Importance: powerful

Recommends: tantan

Recommends: terraphast

Recommends: thesias

Recommends: tiddit

Recommends: toppred

Recommends: transdecoder

Recommends: tnseq-transit

Recommends: tn-seqexplorer

Recommends: toil

Recommends: tombo

Recommends: tortoize

Recommends: tracetuner

Recommends: transrate-tools

Recommends: treeview
X-Category: Visualisation

X-Recommends: treevolve
X-Comment: Homepage of software vanished, packaging in SVN is obviosely stalled
 Feel free to delete the 'X-' in front if you intend to do something on this package

Recommends: trf

Recommends: trinityrnaseq

Recommends: twopaco

Recommends: uc-echo
X-Category: NGS

Recommends: megadepth

Recommends: ufasta

Recommends: umap-learn

Recommends: umis

Recommends: uncalled

Recommends: unicycler

Recommends: unikmer

Recommends: varna

Recommends: varmatch

Recommends: varscan

Recommends: vcfanno

Recommends: vdjtools

Recommends: vg

Recommends: vienna-rna
X-Category: Secondary structure of nucleic acids

Recommends: virulencefinder

Recommends: vmatch

Recommends: vmd

Recommends: vsearch

Recommends: vt

Recommends: xpore

Recommends: yaha

Recommends: yanagiba

Recommends: yanosim

Recommends: canu
Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)

Recommends: zodiac-zeden
Language: C, C++

Recommends: discosnp, mapsembler2

Recommends: dnaclust

Recommends: r-cran-tcr, r-cran-tigger, r-cran-alakazam, r-cran-shazam, igor, r-cran-sdmtools, presto, changeo

Recommends: igblast

Recommends: pigx-rnaseq, pigx-scrnaseq

X-Mark: The information below needs to be checked whether it can be obtained from Vcs or needs to stay here

Recommends: copycat
Homepage: http://www-ab.informatik.uni-tuebingen.de/software/copycat/welcome.html
License: Use of the program is free for academic purposes at an academic institute. For all other uses, please contact the authors.
Pkg-Description: fast access to cophylogenetic analyses
 CopyCat provides an easy and fast access to cophylogenetic analyses.
 It incorporates a wrapper for the program ParaFit, which conducts a
 statistical test for the presence of congruence between host and
 parasite phylogenies. CopyCat offers various features, such as the
 creation of customized host-parasite association data and the
 computation of phylogenetic host/parasite trees based on the NCBI taxonomy.

Recommends: btk-core
Homepage: http://sourceforge.net/projects/btk/
Responsible: Morten Kjeldgaard <mok@bioxray.au.dk>
License: GPL
WNPP: 459753
Pkg-Description: biomolecule Toolkit C++ library
 The Biomolecule Toolkit is a library for modeling biological
 macromolecules such as proteins, DNA and RNA. It provides a C++ interface
 for common tasks in structural biology to facilitate the development of
 molecular modeling, design and analysis tools.

Recommends: asap
Homepage: http://asap.ahabs.wisc.edu/software/asap/
Responsible: Andreas Tille <tille@debian.org>
License: GPL
Pkg-Description: organize the data associated with a genome
 Developments in genome-wide approaches to biological research have
 yielded greatly increased quantities of data, necessitating the cooperation
 of communities of scientists focusing on shared sets of data. ASAP
 leverages the internet and database technologies to meet these needs.
 ASAP is designed to organize the data associated with a genome from the
 early stages of sequence annotation through genetic and biochemical
 characterization, providing a vehicle for ongoing updates of the annotation
 and a repository for genome-scale experimental data. Development was
 motivated by the need to more directly involve a greater community of
 researchers, with their collective expertise, in keeping the genome
 annotation current and to provide a synergistic link between up-to-date
 annotation and functional genomic data. The system is continually under
 development at the Genome Evolution Lab with the stable, in-use, publicly
 available University of Wisconsin installation updated regularly.
 .
 Software development on ASAP began in early 2002, and ASAP has been
 continually improved up until the present day. A longstanding goal of
 the ASAP project was to make the source code of ASAP available so that
 other installations of ASAP could be implemented. As future ASAP
 installations come to pass, ASAP will be further extended to be
 inter-operable between sites.
X-Category: Annotation

Recommends: cactus
Homepage: http://www.cactuscode.org/Community/Biology.html
License: GPL
Pkg-Description:
 Cactus is an open source problem solving environment designed for scientists
 and engineers. Its modular structure easily enables parallel computation
 across different architectures and collaborative code development between
 different groups.
 .
 Cactus provides easy access to many cutting edge software technologies being
 developed in the academic research community, including the Globus
 Metacomputing Toolkit, HDF5 parallel file I/O, the PETSc scientific library,
 adaptive mesh refinement, web interfaces, and advanced visualization tools.

Recommends: contralign
Homepage: http://contra.stanford.edu/contralign/
License: Public Domain
Pkg-Description: parameter learning framework for protein pairwise sequence alignment
 CONTRAlign is an extensible and fully automatic parameter learning
 framework for protein pairwise sequence alignment based on pair
 conditional random fields. The CONTRAlign framework enables the
 development of feature-rich alignment models which generalize well to
 previously unseen sequences and avoid overfitting by controlling model
 complexity through regularization.

Recommends: concavity

Recommends: conservation-code

Recommends: galaxy

Recommends: genographer
Homepage: https://sourceforge.net/projects/genographer/
License: GPL
Pkg-Description: read data and reconstruct them into a gel image
 This program will read in data from an ABI 3700, 3100, 377 or 373,
 CEQ 2000 or SCF and reconstruct them into a gel image which is
 straightened and sized. Bins can be defined easily and viewed as
 thumbnails, which allows for a fairly quick and easy way of scoring a gel.
 .
 The program is written in Java and uses the Java 1.3 API. Therefore,
 it should run on any machine that can run java.

Recommends: phylographer
Homepage: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html
License: GPL
X-Category: Graphical representation of sequence conservation
Language: Tcl/Tk
Pkg-Description: Graph Visualization Tool
 PhyloGrapher is a program designed to visualize and study evolutionary
 relationships within families of homologous genes or proteins
 (elements).  PhyloGrapher is a drawing tool that generates custom graphs
 for a given set of elements. In general, it is possible to use
 PhyloGrapher to visualize any type of relations between elements.
 Used in conjunction with tcl_blast_parser, PhyloGrapher can represent
 the results of a BLAST search as a graph.
 .
 PhyloGrapher and tcl_blast_parser are useful tools to analyse BLAST
 biological sequence alignment reports (BLAST is provided by Debian's
 blast2 package).
Remark: Outdated upstream, better alternatives available
 The former packaging effort of this package was dropped.  It seems
 that http://cytoscape.org/ is a reasonable replacement.

Recommends: phylowin
Homepage: http://pbil.univ-lyon1.fr/software/phylowin.html
WNPP: 395840
License: unknown
Pkg-Description: Graphical interface for molecular phylogenetic inference
 Phylo_win is a graphical colour interface for molecular phylogenetic
 inference. It performs neighbor-joining, parsimony and maximum
 likelihood methods and bootstrap with any of them. Many distances can be
 used including Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy
 (1995), LogDet for nucleotidic sequences, Poisson correction for protein
 sequences, Ka and Ks for codon sequences. Species and sites to include
 in the analysis are selected by mouse. Reconstructed trees can be drawn,
 edited, printed, stored and evaluated according to numerous criteria.
 .
 This program uses sources files from the Phylip program, which forbids
 its use for profit.  Therfore, Phylo_win will unfortunately have to be
 distributed in contrib or non-free.
Remark: Issuer of previous ITP said:
 Because I could never figure out the license of Phylo_win, and because the
 upstream authors released SeaView 4, which provides similar functionalities, I
 will not package Phylo_win.
 .
 Probably it makes sense to remove this project from the prospective packages
 list.

Recommends: phpphylotree
Homepage: http://www.bioinformatics.org/project/?group_id=372
License: GPL
Pkg-Description: draw phylogenetic trees
 PhpPhylotree is a web application that is able to draw phylogenetic trees.
 It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.

Recommends: twain
Homepage: http://cbcb.umd.edu/software/pirate/twain/twain.shtml
License: Open Source
Pkg-Description: syntenic genefinder employing a Generalized Pair Hidden Markov Model
 TWAIN is a new syntenic genefinder which employs a Generalized Pair
 Hidden Markov Model (GPHMM) to predict genes in two closely related
 eukaryotic genomes simultaneously.  It utilizes the MUMmer package to
 perform approximate alignment before applying a GPHMM based on an
 enhanced version of the TigrScan gene finder.  TWAIN was written by
 Bill Majoros and Mihaela Pertea while at The Institute for Genomic
 Research (TIGR).
 .
 TWAIN consists of two components: (1) ROSE, the Region Of Synteny
 Extractor, which identifies contiguous regions likely to contain one
 or more syntenic genes, and (2) OASIS, a generalized pair hidden
 Markov model (GPHMM) for predicting genes in the regions identified
 by ROSE.  The system utilizes approximate alignments constructed by
 the PROmer and NUCmer programs in the MUMmer package to assess
 approximate alignment scores efficiently.  More detailed information
 on the architecture of this system will be made available soon.
 Slides from a talk at Computational Genomics 2004 are now available.
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)

Recommends: rose
Homepage: http://www.cbcb.umd.edu/software/rose/Rose.html
License: Open Source
Pkg-Description: Region-Of-Synteny Extractor
 ROSE is a program which identifies regions between two genomes which
 are likely to contain orthologous genes. The two genomes are given as
 two multi fasta files of DNA sequences. The PROmer program from the
 MUMmer package needs to be run first between the two genomes, and the
 resulting delta file is then input to ROSE. If a previous annotation
 is available for one or both genomes, then the coordinates of the
 annotated genes from a genome can be optionally given as input in a
 gff file. The gene coordinates will be used to guide the length of
 the regions produced by ROSE. By default, when finding a region of
 consistent alignments, ROSE will add a user-defined margin (1000 bp
 by default) on either side of that region. When a predicted gene
 overlaps an alignment we use the gene prediction to extend the
 boundaries of the output region.
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)

Recommends: glimmerhmm
Homepage: http://www.cbcb.umd.edu/software/glimmerhmm/
License: Artistic
Pkg-Description: Eukaryotic Gene-Finding System
 GlimmerHMM is a new gene finder based on a Generalized Hidden Markov
 Model (GHMM). Although the gene finder conforms to the overall
 mathematical framework of a GHMM, additionally it incorporates splice
 site models adapted from the GeneSplicer program and a decision tree
 adapted from GlimmerM. It also utilizes Interpolated Markov Models
 for the coding and noncoding models . Currently, GlimmerHMM's GHMM
 structure includes introns of each phase, intergenic regions, and
 four types of exons (initial, internal, final, and single). A basic
 user manual can be consulted here.
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)

Recommends: genezilla
Homepage: http://www.genezilla.org/
License: Artistic
Language: C++
X-Importance: state-of-art
X-Category: Gene prediction (through GHMM)
Pkg-Description: eukaryotic gene finder
 GeneZilla is a state-of-the-art program for computational prediction
 of protein-coding genes in eukaryotic DNA, and is based on the
 Generalized Hidden Markov Model (GHMM) framework, similar to GENSCAN
 and GENIE. It is highly reconfigurable and includes software for
 retraining by the end-user. It is written in highly optimized C++ and
 runs under most UNIX/Linux platforms. The run time and memory
 requirements are linear in the sequence length, and are in general
 much better than those of competing systems, due to GeneZilla's novel
 decoding algorithm. Graph-theoretic representations of the high
 scoring open reading frames are provided, allowing for exploration of
 sub-optimal gene models. It utilizes Interpolated Markov Models
 (IMMs), Maximal Dependence Decomposition (MDD), and includes states
 for signal peptides, branch points, TATA boxes, CAP sites, and will
 soon model CpG islands as well.
 .
 GeneZilla is an open-source project hosted at bioinformatics.org and
 currently consists of ~20,000 lines of code.  GeneZilla evolved out
 of the ab initio eukaryotic gene finder TIGRscan, which was developed
 at The Institute for Genomic Research over a 3-year period under NIH
 grants R01-LM06845 and R01-LM007938, and which served as the basis
 for the comparative gene finder TWAIN.
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)

Recommends: exalt
Homepage: http://www.cbcb.umd.edu/software/exalt/
License: Artistic
Pkg-Description: phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
 ExAlt is a software program designed to predict alternatively spliced
 overlapping exons in genomic sequence. The program works in several
 ways depending on the available input. ExAlt can use information of
 existing gene structure as well as sequence conservation to improve
 the precision of it's predictions. ExAlt can also make predictions
 when only a single genomic sequence is available. ExAlt has been
 extensively tested on Drosophila melanogaster, but can be adapted to
 run on other species.
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)

Recommends: jigsaw
Homepage: http://www.cbcb.umd.edu/software/jigsaw/
License: Artistic
Pkg-Description: gene prediction using multiple sources of evidence
 JIGSAW is a program designed to use the output from gene finders,
 splice site prediction programs and sequence alignments to predict
 gene models. The program provides an automated way to take advantage
 of the many succsessful methods for computational gene prediction and
 can provide substantial improvements in accuracy over an individual
 gene prediction program.
 .
 JIGSAW is available for all species. It is tested on Human, Rice
 (Oryza sativa), Arabidopsis thaliana , Brugia malayi, Cryptococcus
 neoformans, Entamoeba histolytica, Theileria parva, Aspergillus
 fumigatus, Plasmodium falciparum and Plasmodium yoelii.
 .
 The linear combiner option is now available in the current JIGSAW
 software distribution. This allows JIGSAW to be run without the use
 of training data. A weight is assigned to each evidence source, and
 gene predictions are based on a weighted voting scheme, yielding the
 best 'consensus' predictions.
 .
 Predictions are now available for the ENCODE regions in Human and
 viewable as custom tracks in the UCSC Human Genome
 Browser. Predictions available for the Human genome and viewable as
 custom tracks in the UCSC Human Genome Browser
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)

Recommends: genesplicer
Homepage: http://www.cbcb.umd.edu/software/GeneSplicer/
License: Artistic
Pkg-Description: computational method for splice site prediction
 A fast, flexible system for detecting splice sites in the genomic DNA
 of various eukaryotes. The system has been trained and tested
 successfully on Plasmodium falciparum (malaria), Arabidopsis
 thaliana, human, Drosophila, and rice . Training data sets for human
 and Arabidopsis thaliana are included. Use the GeneSplicer Web
 Interface to run GeneSplicer directly, or see below for instructions
 on downloading the complete system including source code.
 .
 There is no independent program to train GeneSplicer, but there is a
 way to obtain the necessary files by using the training procedure of
 GlimmerHMM.
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)

Ignore: riso
Homepage: http://kdbio.inesc-id.pt/~asmc/software/riso.html
License: not specified
Pkg-Description: motif discovery tool
 RISO discovers motifs composed of many binding sites separated by
 spacers. Each binding site is called a box
 .
 The author of SMILE claims at his homepage
 http://www-igm.univ-mlv.fr/~marsan/smile_english.html that RISO is
 faster and more powerfull than SMILE which is described itself as
 "SMILE is a tool that infers motifs in a set of sequences, according
 to some criterias. It was first made to infer exceptionnal sites as
 binding sites in DNA sequences. It allows to infer motifs written on
 any alphabet (even degenerate) in any kind of sequences.  The
 specificity of SMILE is to allow  to deal with what we call
 "structured motifs",  which are motifs associated by some distance
 constraints. In particular, SMILE is able to group under a unique
 model different occurrences composed of several boxes separated by
 spacers of different lengths."
 .
 The reference to SMILE is made here especially because there is some
 work done in the Debian Med SVN at
 http://svn.debian.org/wsvn/debian-med/trunk/packages/smile/trunk/
 .
 On the other hand the SMILE author told us in private mail that he
 thinks that RISO is dead and SMILE continues to have some importance.

Recommends: mummergpu
Homepage: http://mummergpu.sourceforge.net/
License: Artistic
Pkg-Description: High-throughput sequence alignment using Graphics Processing Units
 The recent availability of new, less expensive high-throughput DNA
 sequencing technologies has yielded a dramatic increase in the volume
 of sequence data that must be analyzed. These data are being
 generated for several purposes, including genotyping, genome
 resequencing, metagenomics, and de novo genome assembly
 projects. Sequence alignment programs such as MUMmer have proven
 essential for analysis of these data, but researchers will need ever
 faster, high-throughput alignment tools running on inexpensive
 hardware to keep up with new sequence technologies.
 .
 MUMmerGPU is a low cost, ultra-fast sequence alignment program
 designed to handle the increasing volume of data produced by new,
 high-throughput sequencing technologies. MUMmerGPU is a GPGPU drop-in
 replacement for MUMmer, using the GPUs in common workstations to
 simultaneously align multiple query sequences against a single
 reference sequence stored as a suffix tree. By processing the queries
 in parallel on the highly parallel graphics card, MUMmerGPU achieves
 more than a 10-fold speedup over a serial CPU version of the sequence
 alignment kernel, and outperforms MUMmer on a high end CPU by
 3.5-fold in total application time when aligning reads from recent
 sequencing projects using Solexa/Illumina, 454, and Sanger sequencing
 technologies.
Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)

Recommends: amoscmp
Homepage: http://amos.sourceforge.net/docs/pipeline/AMOScmp.html
License: Artistic
Pkg-Description: comparative genome assembly package
 A comparative assembler is a program that can assemble a set of
 shotgun reads from an organism by mapping them to the finished
 sequence of a related organism. Thus, a comparative assembler
 transforms the traditional overlap-layout-consensus approach to
 alignment-layout-consensus. The AMOScmp package uses the MUMmer
 program to perform a mapping of the reads to the reference genome,
 then processes the alignment results with a sophisticated layout
 program designed to take into account polymorphisms between the two
 genomes. For a detailed description of the algorithms involved please
 refer to the paper listed in the References section.
 .
 AMOScmp uses as AMOS messages as both the inputs and the outputs (see
 documentation). Two utilities are provided to process these files:
 tarchive2amos - a versatile converter from trace archive .seq, .qual,
 and .xml information into AMOS formatted data; amos2ace - a converter
 from AMOS formatted data to the .ACE assembly format. In addition,
 the AMOS::AmosLib Perl module is provided as a tool for users who
 prefer to write their own conversion utilities. Please see the
 documentation included with the distribution for more information.
 .
 AMOScmp is part of the AMOS package (see
 http://amos.sourceforge.net/)- a collaborative effort to develop a
 modular open-source framework for assembly development.
Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)

Recommends: minimus
Homepage: http://amos.sourceforge.net/docs/pipeline/minimus.html
License: Artistic
Pkg-Description: AMOS lightweight assembler
 minimus is an assembly pipeline designed specifically for small
 data-sets, such as the set of reads covering a specific gene. Note
 that the code will work for larger assemblies (we have used it to
 assemble bacterial genomes), however, due to its stringency, the
 resulting assembly will be highly fragmented. For large and/or
 complex assemblies the execution of Minimus should be followed by
 additional processing steps, such as scaffolding.
 .
 minimus follows the Overlap-Layout-Consensus paradigm and consists of three main modules:
  * overlapper - computes the overlaps between the reads using a
    modified version of the Smith-Waterman local alignment algorithm
  * tigger - uses the read overlaps to generate the layouts of reads
    representing individual contigs
  * make-consensus - refines the layouts produced by the tigger to
    generate accurate multiple alignments within the reads
 .
 minimus uses as AMOS messages as both the inputs and the outputs (see
 documentation). Two utilities are provided to process these files:
 tarchive2amos - a versatile converter from trace archive .seq, .qual,
 and .xml information into AMOS formatted data; amos2ace - a converter
 from AMOS formatted data to the .ACE assembly format. In addition,
 the AMOS::AmosLib Perl module is provided as a tool for users who
 prefer to write their own conversion utilities. Please see the
 documentation included with the distribution for more information.
 .
 minimus is part of the AMOS package - a collaborative effort to
 develop a modular open-source framework for assembly development.
Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)

Ignore: catissuecore
Homepage: https://cabig.nci.nih.gov/tools/catissuecore
License: to be clarified, NCICB Open Source Project Site
Pkg-Description: biospecimen inventory, tracking, and basic annotation
 caTissue Core is caBIG's tissue bank repository tool for biospecimen
 inventory, tracking, and basic annotation. Version 1.2.1 of caTissue
 permits users to track the collection, storage, quality assurance,
 and distribution of specimens as well as the derivation and
 aliquotting of new specimens from an existing ones (e.g. for DNA
 analysis). It also allows users to find and request specimens that
 may then be used in molecular, correlative studies.
 .
 Intended Audiences: Translational Researchers, Pathologists, Biobank
 Managers
Remark: A lot of stuff can be found at National Cancer Institute's
 Center for Bioinformatics (NCICB) Open Source Project Site
 http://gforge.nci.nih.gov/ which has to be evaluated and put into the
 right category of our tasks files

Ignore: trapss
Homepage: https://putt.eng.uiowa.edu/
License: Creative Commons for Science license
Pkg-Description: Transcript Annotation Prioritization and Screening System
 TrAPSS stands for Transcript Annotation Prioritization and Screening
 System. It is a system comprised of several tools written by
 researchers at the Coordinated Lab for Computational Genomics in the
 University of Iowa. The system aims to aid scientists who are
 searching for the genetic mutation or mutations that are linked to
 expression of a disease phentotype. The system offers support for
 almost all areas of a mutation discovery project from the creation
 and prioritization of a large candidate gene list, to the selection,
 ordering, and managing of primer pairs, and even support for SSCP
 assay results. TrAPSS is a currently deployed and often used tool for
 several laboratories here at the University of Iowa in the College of
 Medicine. The system is composed of several Java applications, many
 web-based PHP tools, and a local MySQL database. Even the Java
 applications are available through a web browser due to Sun's Java
 Web Start. Director of the CLCG, Professor Terry A. Braun, heads the
 project along with Dr. Todd Scheetz and Prof. Thomas
 L. Casavant. Eight developers create and maintain the software:
 Bartley Brown , Hakeem Almabrazi, Steven Davis and Jason Grundstad;
 along with three graduate students, Brian O'Leary, John Ritchison and
 Michael Smith; and one undergraduate student, Matthew Kemp.
 Importance of TrAPSS
 .
 The true importance of TrAPSS is that it is based upon a novel way to
 examine a large candidate list of genes. Rather than sequentially
 examining full genes, the scheme often followed in current target
 identification projects, TrAPSS provides tools that offer the user
 the opportunity to screen certain small parts of several genes from
 the candidate list at once. This "parallel" screening idea was
 envisioned by researchers here at the University of Iowa including
 Dr. Edwin Stone and Prof. Thomas L. Casavant. Research by graduate
 students Steven Davis and Brian O'Leary has demonstrated the
 advantage of the parallel screening method over the sequential
 sequencing of large candidate lists.
Remark: Found at
 http://gforge.nci.nih.gov/softwaremap/trove_list.php?form_cat=337

Recommends: bambus
Homepage: http://amos.sourceforge.net/docs/bambus/
License: Artistic
Pkg-Description: hierarchical approach to building contig scaffolds
 BAMBUS is the first publicly available scaffolding program. It orders
 and orients contigs into scaffolds based on various types of linking
 information. Additionally, BAMBUS allows the users to build scaffolds
 in a hierarchical fashion by prioritizing the order in which links
 are used. For more information please check out the online
 documentation.
 .
 Note that currently Bambus is undergoing a transition in order to be
 integrated with the AMOS package (see http://amos.sourceforge.net/)
Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)

Recommends: gmv
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?GMV
License: GPL
Pkg-Description: comparative genome browser for Murasaki
 GMV is a comparative genome browser for Murasaki. GMV visualizes
 anchors from Murasaki, annotation data from GenBank files, and
 expression / prediction score from GFF files.

Recommends: pyrophosphate-tools
Homepage: http://www-naweb.iaea.org/nafa/ipc/public/d4_pbl_6a.html
License: not specified
Pkg-Description: for assembling and searching pyrophosphate sequence data
 Simple tools for assembling and searching high-density picolitre
 pyrophosphate sequence data.

Recommends: figaro
Homepage: http://amos.sourceforge.net/Figaro/Figaro.html
License: Artistic
Pkg-Description: novel vector trimming software
 Figaro is a software tool for identifying and removing the vector
 from raw DNA sequence data without prior knowledge of the vector
 sequence.  By statistically modeling short oligonucleotide
 frequencies within a set of reads, Figaro is able to determine which
 DNA words are most likely associated with vector sequence.  For a
 description of Figaro's algorithms please see our paper.  Figaro is
 part of the AMOS suite.
Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)

Recommends: mirbase
Homepage: http://microrna.sanger.ac.uk/
License: Public Domain
WNPP: 420938
Responsible: Charles Plessy <plessy@debian.org>
Pkg-Description: The microRNA sequence database
 The miRBase Sequence Database provides a searchable repository
 for published microRNA sequences and associated annotation,
 functionality previously provided by the microRNA Registry.  miRBase
 also contains predicted miRNA target genes in miRBase Targets, and
 provides a gene naming and nomenclature function in the miRBase
 Registry.
 .
 Release 9.1 of the database contains 4449 entries representing hairpin
 precursor miRNAs, expressing 4274 mature miRNA products, in primates,
 rodents, birds, fish, worms, flies, plants and viruses.
 .
 This package will install the miRBase database for mySQL, EMBOSS, and/or
 ncbi-blast if you have the corresponding packages installed.
 .
 It is possible that mirbase will not be a package from the main archive, but
 will be autogenerated as part of a larger data packaging effort.

X-Recommends: repeatfinder
X-Homepage: http://www.cbcb.umd.edu/software/RepeatFinder/
X-License: Artistic
X-Pkg-Description: finding repetitive sequences complete and draft genomes
 Two programs for finding repeats in genomic DNA sequences.  The first
 program, described in the paper by Volfovsky et al. (2001) Genome
 Biology is RepeatFinder.  A second program, designed specifically to
 find repeats likely to confuse a genome assembly, is called
 ClosureRepeatFinder.  The two programs are quite different and have
 different purposes; RepeatFinder is intended to be the more
 comprehensive approach.  Note that RepeatFinder depends on Stefan
 Kurtz's REPuter.
X-Note: Depends from non-distributable code reputer (see below)

X-Recommends: reputer
X-Homepage: http://citeseer.ist.psu.edu/kurtz95reputer.html
X-License: non-commercial
X-Pkg-Description: fast computation of maximal repeats in complete genomes
 A software tool was implemented that computes exact repeats and
 palindromes in entire genomes very efficiently.
X-Note: Code is not redistributable see mailing list discussion at
 http://lists.debian.org/debian-med/2012/07/msg00195.html

Recommends: uniprime
Homepage: http://code.google.com/p/uniprime/
License: GPL-3+
Responsible: Charles Plessy <plessy@debian.org>
Pkg-Description: workflow-based platform for universal primer design
 UniPrime automatically designs large sets of universal primers by simply
 inputting a GeneID reference. It automatically retrieves and aligns
 orthologous sequences from GenBank, identifies regions of conservation within
 the alignment and generates suitable primers that can amplify variable genomic
 regions. UniPrime differs from previous automatic primer design programs in
 that all steps of primer design are automated, saved and are phylogenetically
 limited. We have experimentally verified the efficiency and success of this
 program. UniPrime is an experimentally validated, fully automated program that
 generates successful cross-species primers that take into account the
 biological aspects of the PCR.

Recommends: genetrack
Homepage: http://sysbio.bx.psu.edu/genetrack.html
License: MIT
Responsible: Charles Plessy <plessy@debian.org>
Pkg-Description: genomic data storage and visualization framework
 GeneTrack is a high performance bioinformatics data storage and analysis
 system designed to store genome wide information. It is currently used to
 analyze data obtained via high-throughput rapid sequencing platforms such as
 the 454 and Solexa as well as tiling array data based on various platforms.

Recommends: operondb
Homepage: http://www.cbcb.umd.edu/cgi-bin/operons/operons.cgi
License: to be clarified
Pkg-Description: detect and analyze conserved gene pairs
 Comparison of complete microbial genomes reveals a large number of
 conserved gene clusters - sets of genes that have the same order in
 two or more different genomes. Such gene clusters often, but not
 always represent a co-transcribed unit, or operon. A method was
 developed to detect and analyze conserved gene pairs - pairs of genes
 that are located close on the same DNA strand in two or more
 bacterial genomes. For each conserved gene pair, an estimate of
 probability is calculated that the genes belong to the same
 operon. The algorithm takes into account several alternative
 possibilities. One is that functionally unrelated genes may have the
 same order due simply because they were adjacent in a common
 ancestor. Other possibilities are that genes may be adjacent in two
 genomes by chance alone, or due to horizontal transfer of the gene
 pair.
 .
 The method is modified from the one described in: Maria D. Ermolaeva,
 Owen White and Steven L. Salzberg. Prediction of Operons in Microbial
 Genomes. Nucleic Acids Research, 29, 1216-1221, (2001)
 .
 OperonDB was supported by the NIH under grant R01-LM007938 and by the
 NSF under grant DBI-0234704.
Remark: Other sequence analysis tools (http://www.cbcb.umd.edu/software/);
 no info about license or downloadable code found, but tried to
 contact authors.

Recommends: trnascan-se

Comment: If you stumble upon alfresco at
 http://www.sanger.ac.uk/Software/Alfresco/ - it seems outdated and
 tarball vanished from the downlowad page.  So this is not for us even
 if it is linked from Sanger Institute web site.

Comment: If you stumble upon angler at
 http://www.sanger.ac.uk/Software/Angler/ - it seems outdated because
 it is not updated since 1997.  I found no license statement and so
 this is probably also not for us except somebody has real interest
 and volunteers to clarify the license.

Recommends: cdna-db
Homepage: http://www.sanger.ac.uk/Software/analysis/cdna_db/
License: Artistic
Pkg-Description: quality-control checking of finished cDNA clone sequences
 cdna_db is a software system designed for quality-control checking of
 finished cDNA clone sequences, and their computational analysis. The
 combination of a relational db (MySQL) schema, and an
 object-orientated perl API make it easy to implement high-level
 analyses of these transcript sequences.
 .
 The cdna_db can store cDNA clone sequences, and ESTs and
 consensus/contig sequences also derived from these clones. These are
 then used by the system to check cDNA clone sequence identity etc
 (see deneral_doc.txt). For each clone multiple DNA sequence versions
 can be stored, if for instance, the finished DNA sequence is revised
 as part of the sequencing process.
 .
 A blast pipeline is implemented together with a job control system
 (with LSF underlying) so that multiple CPUs can be used in parallel
 to carry out the blasts of large datasets. The searches can be made
 incremental, so as more cDNA sequences are added to the databank,
 just the new clones are blasted.
 .
 Utility scripts are provided to delete previous search results, and
 dump cDNA clones sequences (such as those that passed the QC
 checking) from the cdna_db.

Recommends: coot

Recommends: caftools

Recommends: roche454ace2caf
Homepage: http://genome.imb-jena.de/software/roche454ace2caf/
License: not specified
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: convert GS20 or FLX assemblies into CAF format
 Some tools to convert GS20 or FLX assemblies (454Contigs.ace) into
 CAF format so that these are correct viewable/editable/... whithin
 the staden package (gap4).  You have then access to "hidden data",
 exact aligned trace and there positions, base values etc and whith
 staden-1-7-0 you have graphical access to the associated flowgramm
 traces (SFF format).
 .
 Description, Goals - please take a look at
 http://genome.imb-jena.de/software/roche454ace2caf/Poster_UserMeeting_GS20_Munich_070328.pdf
Remark: The BioLinux distribution http://envgen.nox.ac.uk/biolinux.html
 maintains a package called bio-linux-assembly-conversion-tools which
 contains caftools and roche2gap in one package with the following
 description:
 .
 Conversion tools for handling 454 assemblies.
 .
 This package contains code from different authors that allow sequence
 assemblies to be converted into formats such as CAF (Common Assembly
 Format) or GAP4. This package includes tools to convert assemblies
 from Newbler's ace format for loading into a gap4 assembly.

Recommends: big-blast
Homepage: ftp://ftp.sanger.ac.uk/pub/pathogens/software/artemis/extra/big_blast.pl
License: not specified
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: Helper tool to run blast on large sequences
 This script will chop up a large sequence, run blast on each bit and
 then write out an EMBL feature table and a MSPcrunch -d file
 containing the hits.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Recommends: estferret
Homepage: http://legr.liv.ac.uk/EST-ferret/index.htm
License: to be clarified
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: processes, clusters and annotates EST data
 ESTFerret processes, clusters and annotates EST data. It is
 user-configurable. Results are currently stored in a series of text
 tables. Annotation consists of searches against use r-defined blast
 databases, prosite, GO and allocation of EC numbers where possible.
 .
 EST-ferret is a user-configurable, automated pipeline for the
 convenient analysis of EST sequence data that includes all of the
 necessary steps for cleanup and trimming, submission to external
 sequence repositories, clustering, identification by BLAST homology
 searches and by searches of protein domain databases, annotation with
 computer-addressable terms and production of outputs for direct entry
 into microarray analysis packages. It is composed of several widely
 used, open-source algorithms, including PHRED, CAP3, BLAST, and a
 range of sequence and annotation databases, including Gene Ontology
 and Conserved Domain Database to deliver a putative identity and a
 detailed annotation of each clone. It can be run either step-by-step
 to track the outputs, or as a single batch process. Users can easily
 edit the configuration file to define parameter settings.
 .
 This package has five major components: (1) ESTs coding system; (2)
 sequence processing; (3) sequence clustering; (4) sequence annotating
 and (5) storage and reporting of results. DNA trace files are renamed
 and converted into FASTA format, cleaned and submitted to
 dbEST(Boguski, et al, 1993). Sequence assembly uses two rounds of
 CAP3 to assemble the ESTs into groups corresponding to separate gene
 families and unique genes. Sequence identification and annotation is
 provided by a series of BLAST homology searches (Parallel_BLAST and
 Priority_BLAST) against user-defined sequence databases implemented
 with the NCBI BLASTALL algorithm. The BLAST results are parsed and
 annotation terms that reflect functional attributes are captured from
 Gene Ontology (The Gene Ontology Consortium, 2000), KEGG and Enzyme
 Commission (EC) databases and applied to each of the clones. CDD (and
 InterPro) searches are performed for seeking protein domains in the
 sequences. Other options are provided to run PatSearch, RepeatMasker
 and BLAT to find UTRs, repeats and EST candidates in
 genomes. Finally, the package generates analysis reports in a variety
 of flat file formats, sources of which can be serve as inputs for
 some gene annotation and gene expression profiling tools, and also as
 a MySQL database or web-browsable search tool.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Recommends: lamarc

Recommends: lucy

Recommends: maxd
Homepage: http://www.bioinf.man.ac.uk/microarray/maxd/
License: Artistic
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: data warehouse and visualisation environment for genomic expression data
 Maxd is a data warehouse and visualisation environment for genomic
 expression data. It is being developed in the University of
 Manchester by the Microarray Bioinformatics Group.
 .
 Software components:
  maxdLoad2 - standards-compliant, highly customisable transcriptomics
              database
  maxdView  - modular and easily extensible data visualisation and
              analysis environment
  maxdSetup - installation management utility
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Recommends: mesquite

Recommends: migrate
Homepage: http://popgen.scs.fsu.edu/Migrate-n.html
License: to be clarified
Responsible: BioLinux - Nathan S Haigh <n.haigh@sheffield.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: estimation of population sizes and gene flow using the coalescent
 Migrate estimates effective population sizes and past migration rates
 between n population assuming a migration matrix model with
 asymmetric migration rates and different subpopulation sizes. Migrate
 uses maximum likelihood or Bayesian inference to jointly estimate all
 parameters. It can use the followind data types: sequence data using
 Felsenstein's 84 model with or without site rate variation, single
 nucleotide polymorphism data, microsatellite data using a stepwise
 mutation model or a brownian motion mutation model, and
 electrophoretic data using an 'infinite' allele model. The output can
 contain: Estimates of all migration rates and all population sizes,
 assuming constant mutation rates among loci or a gamma distributed
 mutation rate among loci. Profile likelihood tables, Percentiles,
 Likelihood-ratio tests, and simple plots of the log-likelihood
 surfaces for all populations and all loci.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Recommends: msatfinder
Homepage: http://www.genomics.ceh.ac.uk/msatfinder/
License: GPL
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: identification and characterization of microsatellites in a comparative genomic context
 Msatfinder is a Perl script designed to allow the identification and
 characterization of microsatellites in a comparative genomic
 context. There is also an online manual, a discussion forum and an
 online interface where users can do searches in any number of DNA or
 protein sequences (as long as the maximum size of all sequences does
 not exceed 10MB). Nucleotide and amino acid sequences in GenBank,
 FASTA, EMBL and Swissprot formats are supported.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Recommends: oligoarrayaux
Homepage: http://dinamelt.bioinfo.rpi.edu/OligoArrayAux.php
License: non-free (fre academical use)
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: Prediction of Melting Profiles for Nucleic Acids
 OligoArrayAux is a subset of the UNAFold package for use with
 OligoArray (http://berry.engin.umich.edu/oligoarray2_1/). OligoArray
 is a free software that computes gene specific oligonucleotides for
 genome-scale oligonucleotide microarray construction.  (It is not
 really specified what they mean with "free software". You can
 download the source code after registration: "registration is the
 only way for me to keep trace of OligoArray users and be able to send
 you a bug fix or a new release".)
 .
 The original UNAFold server is available at
 http://dinamelt.bioinfo.rpi.edu/download.php and you should probably
 read http://dinamelt.bioinfo.rpi.edu/ if you want to know more about
 "Prediction of Melting Profiles for Nucleic Acids".
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
 Finally it is hard to find some documentation what OligoArrayAux is
 really doing because it is only specified into relation to OligoArray
 (as precondition) and UNAFold (as subset of this) but BioLinux
 distribution http://envgen.nox.ac.uk/biolinux.html decided to package
 this and so it might make soem sense to list it here - further
 investigation is needed.

Recommends: partigene
Homepage: http://www.nematodes.org/bioinformatics/PartiGene/
License: GPL
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: generating partial gemomes
 PartiGene is part of the Edinburgh-EGTDC developed EST-software
 pipeline at the moment consisting of trace2dbEST, PartiGene,
 wwwPartiGene, port4EST and annot8r. PartiGene is a menu-driven,
 multi-step software tool which takes sequences (usually ESTs) and
 creates a dataabase of a non-redundant set of sequence objects
 (putative genes) which we term a partial genome.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Recommends: pfaat
Homepage: http://pfaat.sourceforge.net/
License: GPL
Responsible: BioLinux - Dan Swan <dswan@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: Protein Family Alignment Annotation Tool
 Pfaat is a Java application that allows one to edit, analyze, and
 annotate multiple sequence alignments. The annotation features are a
 key component as they provide a framework to for further sequence,
 structure and statistical analysis.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Comment: priam
 BioLinux contains a priam package which is available at
 http://bioinfo.genotoul.fr/priam/REL_JUL06/index_jul06.html but this
 project has only a "free as in beer" binary download - so this is not
 for us ...

Recommends: prot4est
Homepage: http://xyala.cap.ed.ac.uk/bioinformatics/prot4EST/index.shtml
License: GPL
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: EST protein translation suite
 prot4EST is a perl script that takes expressed sequence tags (ESTs)
 and translates them optimally to produce putative peptides. prot4EST
 intergrates a number of programs to overcome problems inherent with
 translating ESTs.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Recommends: qtlcart
Homepage: http://statgen.ncsu.edu/qtlcart/
License: GPL
Responsible: BioLinux - Dan Swan <dswan@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: map quantitative traits using a map of molecular markers
 QTL Cartographer is a suite of programs to map quantitative traits
 using a map of molecular markers. It contains a set of programs that
 will aid in locating the genes that control quantitative traits using
 a molecular map of markers.  It includes some programs to allow
 simulation studies of experiments.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Recommends: rbs-finder
Homepage: http://www.genomics.jhu.edu/RBSfinder/
License: not specified
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: find ribosome binding sites(RBS)
 The program implements an algorithm to find ribosome binding
 sites(RBS) in the upstream regions of the genes annotated by
 Glimmer2, GeneMark, or other prokaryotic gene finders.  If there is
 no RBS-like patterns in this region, program searches for a start
 codon having a RBS-like pattern ,in the same reading frame upstream
 or downstream and relocates start codon accordingly.
 .
 You can find more detailed information at
 http://nbc11.biologie.uni-kl.de/docbook/doc_userguide_bioinformatics_server/chunk/ch01s06.html
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Recommends: splitstree
Homepage: http://www-ab.informatik.uni-tuebingen.de/software/splitstree3/welcome.html
License: to be clarified
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: Analyzing and Visualizing Evolutionary Data
 Evolutionary data is most often presented as a phylogentic tree, the
 underlying assumption being that evolution is a branching
 process. However, real data is never ideal and thus doesn't always
 support a unique tree, but often supports more than one possible
 tree. Hence, it makes sense to consider tree reconstruction methods
 that produce a tree, if the given data heavily favors one tree over
 all others, but otherwise produces a more general graph that
 indicates different possible phylogenies. One such method is the
 Split Decomposition introduced by Hans-Juergen Bandelt and Andreas
 Dress (1992) and its variations. Another example is Spectral Analysis
 developed by Hendy, Penny and others.
 .
 These and other methods are implemented in the program SplitsTree,
 that I wrote with contributions from Dave Bryant, Mike Hendy, Holger
 Paschke, Dave Penny and Udo Toenges. It is based on the Nexus
 format.
 .
 Note: There is a new version 4.0 written from scratch at
 http://www.splitstree.org/ which requires a license key - so this is
 probably non-free.  Version 3.2 which is linked above has some
 downloadable source code without any license or copyright statement -
 so it has to be clarified whether we are able to distribute this code
 or not.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html


Recommends: taverna
Homepage: http://taverna.sourceforge.net/
License: LGPL
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: designing and executing myGrid workflows for bioinformatics
 The Taverna workbench is a free software tool for designing and
 executing workflows, created by the myGrid  project, and funded
 through OMII-UK. Taverna allows users to integrate many different
 software tools, including web services, such as those provided by the
 National Center for Biotechnology Information, The European
 Bioinformatics Institute, the DNA Databank of Japan (DDBJ), SoapLab,
 BioMOBY and EMBOSS.
 .
 The Taverna Workbench provides a desktop authoring environment and
 enactment engine for scientific workflows expressed in Scufl (Simple
 Conceptual Unified Flow language). The Taverna enactment engine is
 also available separately, and other Scufl enactors are available
 including Moteur. The myExperiment social web site supports finding
 and sharing of workflows and has special support for Scufl
 workflows. The Taverna workbench, myExperiment and associated
 components are developed and maintained by the myGrid team, in
 collaboration with the open source community.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Recommends: taxinspector
Homepage: http://nebc.nox.ac.uk/projects/taxinspector.html
License: Artistic + other free licenses
Responsible: BioLinux - Tim Booth <tbooth@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: browser for entries in the NCBI taxonomy
 TaxInspector is a browser for entries in the NCBI taxonomy. It is
 designed to run as a plugin to annotation software such as maxdLoad2
 and Pedro, but also has a standalone mode.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Recommends: tetra
Homepage: http://www.megx.net/tetra/
License: free academic
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: tetranucleotide frequency calculator
 The TETRA program can be used to calculate how well tetranucleotide
 usage patterns in DNA sequences correlate. Such correlations can
 provide valuable hints on the relatedne ss of DNA sequences, and are
 particularly useful for metagenomic sequences.
Remark: for the Linux version
 Version 1.0.2 (Mac OSX has version
 2.0b30) is deprecated and hence a feature-limited version of
 TETRA. At the time writing, no decisions have been made about
 adapting and cross-compiling the Mac OS X code for this platform. A
 Linux version might happen when REALbasic's Linux IDE is more mature.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Recommends: trace2dbest

Recommends: estscan
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Recommends: profit
WNPP: 525428
Remark: The authors need to change the license, still.

Recommends: obo-edit
Homepage: http://www.geneontology.org
X-Comment: Find the license here [1] and [2].
 [1] http://geneontology.svn.sourceforge.net/viewvc/geneontology/java/oboedit/tags/2.2/release_resources/LICENSE?revision=4863&view=markup
 [2] http://geneontology.svn.sourceforge.net/viewvc/geneontology/java/oboedit/tags/2.2/release_resources/ARTISTIC_LICENSE?revision=4863&view=markup
License: Artistic
Pkg-Description: editor for biological ontologies
 (Open Biological Ontologies) Obo-Edit supports the formal representation
 of biological entities and the specification of is-a (specialisation)
 and part-of relations. Amongst the databases cureated by this tool
 is the GeneOntology.

Recommends: phagefinder
Homepage: http://phage-finder.sourceforge.net/
License: GPL
Language: Perl
X-Category: Genomics; Prophage detection in prokaryotes
Pkg-Description: heuristic computer program to identify prophage regions within bacterial genomes
 It uses tab-delimited results from NCBI BLASTALL or WU BLASTP 2.0 searches against a
 collection of bacteriophage protein sequences and results from HMMSEARCH analysis of
 441 phage-specific HMMs to locate prophage regions. By using FASTA33, MUMMER  or BLASTN,
 it can find potential attachment (att) sites of the phage region(s). Data from tRNAscan-SE
 and Aragorn  are used to determine whether a tRNA  or tmRNA  served as the putative target
 for integration. Additionally, by looking for the presence or absence of specific proteins
 using specific HMM models, Phage_Finder can predict whether the region is most likely
 prophage and which type (Mu, P2, or retron R73), an integrated element, a plasmid, or a
 degenerate phage region.
 .
 The goal of this project is to provide an open-sourced, standardized and automated system
 to identify and classify prophages within prokaryotic genomes. It is hoped that this package
 will facilitate future studies on the biology and evolution of these prophages by providing
 a level of microbial genome annotation that was previously void.

Recommends: treebuilder3d
Homepage: http://www.bcgsc.ca/platform/bioinfo/software/treebuilder
License: GPL
Language: Java
X-Category: Clustering; SAGE expression
Pkg-Description: viewer of SAGE and other types of gene expression data
 TreeBuilder3D is an interactive viewer that allows organization of SAGE and other
 types of gene expression data such as microarrays into hierarchical dendrograms,
 or phenetic networks (the term 'phenetic' used as the analysis relies on principals,
 used in phylogenetic analysis by system biology). Might be used as a visual aid when
 analyzing differences in expression profiles of SAGE libraries, serves as an
 alternative to Venn diagrams.

Recommends: excavator
Homepage: http://csbl.bmb.uga.edu/downloads/excavator/
License: GPL
Language: Java
X-Category: Clustering; Gene expression data
Pkg-Description: gene expression data clustering
 Excavator is a program for gene expression data clustering. It uses a set of unique
 clustering algorithms developed by the Computational Systems Biology Lab (CSBL) at
 the University of Georgia. Excavator represents data internally as a minimum spanning
 tree and outputs results to the user through the use of a micro-array data window,
 graphs, and a dendrogram viewer.
 .
 Features
  * partitioning gene expressions profiles using multiple methods of clustering and
    definitions of distance between profiles.
  * automatic selection of the most plausible number of clusters in a data set
  * three different ways of viewing data: Micro-array, Gene Expression, and Dendrogram.
    As well as graphing individual genes from each cluster independently.
  * identification of genes with expression profiles similar to specified seed genes
  * cluster identification from a noisy background
  * numerical comparison between different clustering results of the same data set
  * runnable on command line as well as through a Java GUI

Recommends: abacas

Recommends: profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun

Recommends: profphd-net, profphd-utils

Recommends: profphd

Recommends: abyss

Recommends: ampliconnoise

Recommends: disulfinder

Recommends: circos, runcircos-gui

Recommends: populations

Recommends: racon, spoa, rampler

Recommends: librg-utils-perl

Recommends: snap

Recommends: pyvcf, vcftools

Recommends: beads

Recommends: x-tandem-pipeline
Homepage: http://pappso.inra.fr/bioinfo/xtandempipeline/
License: GPL
Language: Java
Pkg-Description: peptide/protein identification from MS/MS mass spectra
 X!Tandem is an open-source software performing peptide/protein
 identification from MS/MS mass spectra. X!Tandem is fast and accurate,
 but the Global Proteome Machine (GPM) is relatively limited regarding
 the processing of identification results. X!Tandem pipeline is an
 alternative to the installation of the GPM on local servers.  X!Tandem
 pipeline performs database searching and matching on a list of MS/MS
 runs in one shot, using a list of easily user selected paramaters and
 databases.  X!Tandem pipeline also performs filtering of data according
 to statistical values at peptide and protein levels. The results are
 stored into TSV (Tab Separated Values) files. Moreover, redundancy of
 protein databases are fully filtered as follows :
  * proteins identified without specific peptides compared to others are
    eliminated;
  * proteins identified with the same pool of peptides are assembled;
  * proteins are grouped by function (identified with at least one common
    peptide), and the specific peptides for each sub-group of proteins are
    indicated.

Suggests: maude

Recommends: forge
Homepage: http://combiol.org/forge/
License: Apache 2.0
Pkg-Description: genome assembler for mixed read types
 Forge Genome Assembler is a parallel, MPI based genome assembler for
 mixed read types.
 .
 Forge is a classic "Overlap layout consensus" genome assembler written
 by Darren Platt and Dirk Evers. Implemented in C++ and using the
 parallel MPI library, it runs on one or more machines in a network and
 can scale to very large numbers of reads provided there is enough
 collective memory on the machines used. It generates a full consensus
 alignment of all reads, can handle mixtures of sanger, 454 and illumina
 reads. There is some support for solid color space and it includes built
 in tools for vector trimming and contamination screening.
 .
 Forge and was originally developed at Exelixis and they have kindly
 agreed to place the software which underwent much subsequent development
 outside Exelixis, into the public domain. Forge works with most of the
 common MPI implementations.
Remark: Competitor to MIRA2 and wgs-assembler
 This package was requested by William Spooner <whs@eaglegenomics.com> as
 a competitor to MIRA2 and wgs-assembler.

Recommends: metarep
License: MIT
Homepage: http://www.jcvi.org/metarep/
Pkg-Description: JCVI Metagenomics Reports
 JCVI Metagenomics Reports (METAREP) is a new open source tool for
 high-performance comparative metagenomics. It provides a suite of web
 based tools to help scientists to view, query, browse and compare
 metagenomics annotation data derived from ORFs called on metagenomics
 reads.
 .
 METAREP supports browsing of functional and taxonomic assignments.
 Users can either specify fields, or logical combinations of fields to
 flexibly filter datasets on the fly. Users can compare multiple datasets
 at various functional and taxonomic levels applying statistical tests as
 well as hierarchical clustering, multidimensional scaling and heatmaps.

Recommends: arachne
Homepage: http://www.broadinstitute.org/crd/wiki/index.php/Arachne
License: free
Pkg-Description: toolkit for Whole Genome Shotgun Assembly
 Arachne is a toolkit developed for Whole Genome Shotgun Assembly.
 Arachne consists of a comprehensive set of modules, including a central
 pipeline (Assemblez) that can be run on almost any genome to produce a
 draft assembly. Arachne's mandate explicitly includes accommodating
 difficult genomes with complications such as extreme size, repeats, and
 high polymorphism rates. In order to construct a reasonably
 well-connected assembly from such tricky genomes, Arachne provides
 further tools that can be used after the main module pipeline.
 .
 The Arachne code package has been under continuous development since
 2000. It began with the classic "overlap-layout-consensus" paradigm and
 has since developed into a vast collection of tools, implemented in
 numerous modules, to analyze, visualize and manipulate assemblies. New
 and improved algorithms are becoming available on a regular basis.

Recommends: maker2
Homepage: http://www.yandell-lab.org/software/maker.html
License: GPL / Artistic
Pkg-Description: annotate genomes and create genome databases
 MAKER is a portable and easily configurable genome annotation pipeline.
 It's purpose is to allow smaller eukaryotic and prokaryotic genome
 projects to independently annotate their genomes and to create genome
 databases. MAKER identifies repeats, aligns ESTs and proteins to a
 genome, produces ab-initio gene predictions and automatically
 synthesizes these data into gene annotations having evidence-based
 quality values. MAKER is also easily trainable: outputs of preliminary
 runs can be used to automatically retrain its gene prediction algorithm,
 producing higher quality gene-models on seusequent runs. MAKER's inputs
 are minimal and its ouputs can be directly loaded into a GMOD database.
 They can also be viewed in the Apollo genome browser; this feature of
 MAKER provides an easy means to annotate, view and edit individual
 contigs and BACs without the overhead of a database. MAKER should prove
 especially useful for emerging model organism projects with minimal
 bioinformatics expertise and computer resources

Recommends: e-hive
Homepage: http://www.ensembl.org/info/docs/eHive/index.html
License: Not specified
Pkg-Description: distributed processing system based on 'autonomous agents'
 This is a distributed processing system based on 'autonomous agents' and
 Hive behavioural structure of Honey Bees .  It implements all functionality
 of both data-flow graphs and block-branch diagrams which should allow it
 to codify any program, algorithm, or parallel processing job control system.
 It is not bound to any processing 'farm' system and can be adapted to any GRID.

Recommends: cmap
Homepage: http://gmod.org/wiki/CMap
License: Not specified
Pkg-Description: view comparisons of genetic and physical maps
 CMap is a web-based tool that allows users to view comparisons of genetic and
 physical maps. The package also includes tools for curating map data.

Recommends: gbrowse-syn
Homepage: http://gmod.org/wiki/GBrowse_syn
License: Not specified
Pkg-Description: Generic Synteny Browser
 GBrowse_syn, or the Generic Synteny Browser, is a GBrowse-based synteny
 browser designed to display multiple genomes, with a central reference
 species compared to two or more additional species.  It can be used to
 view multiple sequence alignment data, synteny or co-linearity data
 from other sources against genome annotations provided by GBrowse.
 GBrowse_syn is included with the standard GBrowse package (version 1.69 and
 later). Working examples can be seen at TAIR and WormBase.


Recommends: tripal
Homepage: http://tripal.info/
License: GPL ( as Drupal a derivative )
Pkg-Description: collection of Drupal modules for genomic research
 Tripal is a collection of open-source freely available Drupal modules under
 development at CUGI and a member of the GMOD family of tools. Tripal serve
 as a web interface for the GMOD Chado database. Tripal intially started as
 a web front-end for the Marine Genomics Project (MG.org). Work on the
 interface is currently ongoing for the MG.org project as well as the
 Fagaceae Genomics Web, and other CUGI projects. Tripal is currently being
 implemented for the new Cacao Genome Database, and Citrus Genome Database
 and will be used for the Genome Database for Rosaceae. These latter three
 databases are projects of the Main Bioinformatics Laboratory at Washington
 State University

Recommends: genemark
Homepage: http://exon.biology.gatech.edu/
License: Academic License Agreement
Pkg-Description: family of gene prediction programs
 A family of gene prediction programs developed at Georgia Institute of
 Technology, Atlanta, Georgia, USA.

Recommends: annovar
Homepage: http://www.openbioinformatics.org/annovar/
License: Open Source for non-profit
Pkg-Description: annotate genetic variants detected from diverse genomes
 ANNOVAR is an efficient software tool to utilize update-to-date information
 to functionally annotate genetic variants detected from diverse genomes
 (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and
 many others). Given a list of variants with chromosome, start position, end
 position, reference nucleotide and observed nucleotides, ANNOVAR can perform:
 .
  1. Gene-based annotation: identify whether SNPs or CNVs cause protein coding
     changes and the amino acids that are affected. Users can flexibly use RefSeq
     genes, UCSC genes, ENSEMBL genes, GENCODE genes, or many other gene definition
     systems.
  2. Region-based annotations: identify variants in specific genomic regions,
     for example, conserved regions among 44 species, predicted transcription
     factor binding sites, segmental duplication regions, GWAS hits, database
     of genomic variants, DNAse I hypersensitivity sites, ENCODE
     H3K4Me1/H3K4Me3/H3K27Ac/CTCF sites, ChIP-Seq peaks, RNA-Seq peaks, or many
     other annotations on genomic intervals.
  3. Filter-based annotation: identify variants that are reported in dbSNP,
     or identify the subset of common SNPs (MAF>1%) in the 1000 Genome Project,
     or identify subset of non-synonymous SNPs with SIFT score>0.05, or many
     other annotations on specific mutations.
  4. Other functionalities: Retrieve the nucleotide sequence in any
     user-specific genomic positions in batch, identify a candidate gene list
     for Mendelian diseases from exome data, identify a list of SNPs from
     1000 Genomes that are in strong LD with a GWAS hit, and many other
     creative utilities.
 .
 In a modern desktop computer (3GHz Intel Xeon CPU, 8Gb memory), for
 4.7 million variants, ANNOVAR requires ~4 minutes to perform
 gene-based functional annotation, or ~15 minutes to perform stepwise
 "variants reduction" procedure, making it practical to handle hundreds
 of human genomes in a day.

Recommends: python3-orange
License: GPLv3
Homepage: http://orange.biolab.si/
Pkg-URL: http://orange.biolab.si/debian/
Responsible: Mitar <mmitar@gmail.com>
Pkg-Description: Data mining framework
 Orange is a component-based data mining software. It includes a range
 of data visualization, exploration, preprocessing and modeling
 techniques. It can be used through a nice and intuitive user interface
 or, for more advanced users, as a module for Python programming language.

Recommends: tigr-glimmer-mg

Comment: Several related R packages are listed at CRAN:
         http://cran.r-project.org/web/views/Genetics.html
Comment: There is a Gentoo page featuring some projects we do not have mentioned here:
         http://gentoo-overlays.zugaina.org/dberkholz/sci-biology.html.en
Comment: Phylogenie centric Ubuntu derivative with some additional derivatives
	 http://www.eve.ucdavis.edu/rcthomson/phylis/
Comment: SEQanswers: The next generation sequencing community
	 http://seqanswers.com/forums/showthread.php?t=43
Comment: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)