List of software that was liberated due to negotiations of the Debian Med team with the authors

The Debian Med team tries to encourage authors of scientific software to release their code under DFSG free licenses. This page lists some results of this effort.

Software

Debian Med contact

Upstream confirmation

Date

phylip

ePetition

Joe Felsenstein

2014-02-26

seaview

Depends from phylip

Consequence of freeing phylip

2014-02-26

colt

Debian Med list

No response - fixed by removing affected code parts

2015-03-15

f2j

Debian Med list

No response - fixed by removing affected code parts

2016-01-29

beast-mcmc

Depends from colt and f2j

Consequence of freeing colt and f2j

2016-06-02

fsm-lite

Debian Med list

Author added GPL license file

2016-04-13

fastml

Debian Med list

Private mail from Haim Ashkenazy confirming GPL-2

2015-11-18

eigensoft

Debian Med list

Alkes Price

2016-07-18

ABySS

Debian Med list

License changed in tarball after upstream authors agreed

2016-10-31

MALT

Debian Med list

Repository is open

2016-10-11

paml

User forum

GPL

2017-03-21

pal2nal

Debian Med list

Author has changed to GPL

2017-10-10

segemehl

Debian Med list

GPL

2018-10-04

Discussion in progress

Software

Debian Med contact

Status upstream

Date

gblocks

Debian Med list

No answer yet

2011-02-02

blat

Debian Med packaging list

Further discussion

2015-12-11

varscan

Issue on Github

Issue closed

2016-11-01

ffp

Debian Med list

Redirected question to responsible person

2015-11-26

mssstest

Debian Med list

Refused

2016-01-15

cluster3

Debian Med list

Michiel de Hoon

2016-02-01

blimps and sift

Debian Med list

Pauline Ng: Dual license GPL possible

2016-01-15

fastsimcoal2

User forum

Laurent Excoffier: "No source code" without arguments

2016-06-23

trf

Debian Med list

Yozen Hernandez confirmed long term goal to use a free license

2017-10-12

pcma

Debian Med list

No answer yet

2017-01-04

r-cran-locfit

Debian Med listITP #731599

Author vanished

2012-02-21

SignalP

Debian Med list

No answer yet

2017-04-25

GeneMark

Debian Med list

No answer yet

2017-04-25

CARD RGI

Debian Med list

No answer yet

2017-05-12

GMAP

Debian Med list

Discussion

2017-09-04

locfit

Issue on Github

No answer yet

2017-09-06

seq-gen

Issue on Github

No answer yet

2017-09-06

emmax

Debian Med list

No answer yet

2018-02-11

fasta3

Debian Med list

No answer yet

2018-04-19

aparapi

Github issue

No answer yet

2018-05-18

trnascan-se

Debian Med list

No answer yet

2018-08-05

Known, but not pursued

Software

Reason

Genome Analysis Toolkit

Institution commited to non-free licensing of this project.