In a bizarre decision, Springer-owned BMC Evolutionary Biology retracted Gangolf Jobb’s 2004 paper on Treefinder. The decision and associated claims, found ridiculous by the bioinformatics community, are definitely political, because BMC itself has very low standards regarding availability of published materials (explained later in this post). Also, the journal is owned by Springer, whose Nature wing went political in 2008 by endorsing candidate in any election for the first time in its 150 years history. That bad decision likely made them later to filling the journal pages with anti-Russia tirade (check “Russian Government is Beheading Scientists in Red Square Nature Reports”).
The editors of BMC Evolutionary Biology retract this article  due to the decision by the corresponding author, Gangolf Jobb, to change the license to the software described in the article. The software is no longer available to all scientists wishing to use it in certain territories. This breaches the journals editorial policy on software availability  which has been in effect since the time of publication. The other authors of the article, Arndt von Haeseler and Korbinian Strimmer, have no control over the licensing of the software and support the retraction of this article.
Speaking of BMC’s standards on making materials related to papers available, we contacted BMC Genomics four months back to get access to the genome of a genome paper published two years back. Zhanjiang (John) Liu, Associate Vice President for Research & Associate Provost of Auburn university, published a number of papers describing various aspects of the catfish genome over the years, but never bothered to place the genome online. We contacted him over one year back (~July 2014) seeking access to the genome sequence, but he declined. In July 2015, we contacted him again and then contacted BMC Genomics. BMC’s editors asked him to submit the genome in a public database according to journal rules, but he never bothered and neither did his collaborators at USDA. That is how it goes with BMC, where well-connected authors can refuse to submit genome of a genome paper and still get no action taken against them !!!
The above context should help in judging BMC’s claims for retracting the 2004 bioinformatics paper on Treefinder due to non-availability of the software. This claim of non-availability of bioinformatics software 11 years after publication has been found ridiculous by the bioinformatics community.
Moreover, it is puzzling that so many people are concerned about Treefinder given that the program is judged useless by greedy exploitative academic parasite Sandra Baldauf.
Needless to say, if any real political action has to be taken related to this ongoing saga, it should be those like Sandra Baldauf not getting access to any government-funded pension for reasons explained here. That kind of action will make the publicly- funded academic class stand with their real source of funding and not with the government.