beast 1.8 vs beast 2 - both under development?

[chris warth]

Can someone summarize the current development situation between Beast 1.8 hosted at beast-mcmc and beast2 hosted at beast2 ?

Clearly Beast 2 is under active development.  How about Beast 1.8?

Are they both being developed by the same group, or are the two projects taking different paths?

I have found some issues that I think are bugs in the 1.8 release and I'm wondering if it is worth submitting patches.  

Or is this a dead branch that will see no further work?

I apologize if this topic has been well covered already – a quick search didn't turn up anything definitive.

– Chris Warth

   Computational Proteomics Lab

   Fred Hutchinson Cancer Research Center

[Andrew Rambaut]

Dear Chris,

Please do submit bug reports or patches for 1.8. It is still widely used and is installed in some cluster environments.  

Bugs reports can be submitted through the GoogleCode site:

https://code.google.com/p/beast-mcmc/issues/list

Recent development work in 1.x & 2.x can be viewed at:

https://code.google.com/p/beast-mcmc/source/list

&

https://github.com/CompEvol/beast2/commits/master

respectively, although the latter is just for the core with individual add-on modules being developed independently in other repositories. 

Best,

Andrew

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Andrew Rambaut 

Institute for Evolutionary Biology | Centre for Infection, Immunity & Evolution 

Ashworth Laboratories, University of Edinburgh, Edinburgh, EH3 9JT, UK

contact – a.ra...@ed.ac.uk | http://tree.bio.ed.ac.uk | tel +44 131 6508624

[Reena]

Hello,

Along the same lines, are the BEAST 1.X versions going to be completely replaced by BEAST 2? Should we be migrating over to this new version?

Thanks

[Julian W Tang]

Hi Andrew, Alexei,
 
I'm finding something a bit odd here.
 
I've had to download a new copy of Beast v1.8 from: https://code.google.com/p/beast-mcmc/
 
But every time I extract it, I get a pop-up window from my Norton 60 utilities saying that this Trojan programme is attacking my PC. The PC I use to run Beast is not connected to the internet - I transfer the Beast folder using a USB drive to this machine from a laptop connected to the internet. The USB stick could be infected, but this is the same when I open and unzip the run the Beast v1.8 file from the laptop - and it only seems to happen when I unizip/extract the files fro this Beast v 1.8 folder.
 
Also, when I extract the Beast v1.8.zip file, to the default Beast  v1.8.0 folder, I lose the Beast v1.8 icon within this folder so I cannot run Beast anyway.
 
What's going on? I cannot finish my analysis at the moment because of this.
 
Could someone have possibly sabotaged this Beast download website? Or have I got this Trojan infection on all my systems?
 
I'm removing Trojan.ADH.SMH now with help from this website: http://getridofallmalware.blogspot.ca/2014/04/how-to-remove-trojanadhsmh-virus.html, but any other advice on getting Beast v1.8 up and running again would be welcome.
 
Thanks,
 
Julian
 


 

[Andrew Rambaut]

Dear All,

This file has been hosted by GoogleCode since October 2013. On the download page there is a checksum so you can check the file is not being modified after downloading it.

We have also had a report that Symantec detects this as Trojan.ADH.SMH. The Symantec website has some details about this:

http://www.symantec.com/security_response/writeup.jsp?docid=2014-052320-0051-99

"If one or more files on your computer have been classified as having a Trojan.ADH.SMH threat, this indicates that the files have suspicious characteristics and therefore might contain a new or unknown threat. However, given the sensitive nature of this detection technology, it may occasionally identify non-malicious, legitimate software programs that also share these behavioral characteristics. Therefore, it is recommended that users manually check all files detected as Trojan.ADH.SMH by Symantec antivirus products for potential misidentification, and submit any suspect files to Symantec Security Response for further analysis. For instructions on how to do this, read Submit Virus Samples.”

This would suggest that it isn’t a recognised Trojan but some suspicious behaviour. This may be to do with the Windows Executable wrapper we use to launch BEAST (which is a Java program). 

The final thing is that the actual executable was build on a Mac so it couldn’t have been infected at that point (there is the possibility that the wrapper (Launch4J) was infected at source but this is quite widely used and would likely have been noticed.

The other possibility is that something is infecting these files after download. It would be useful if Windows users could run their anti-viral software and report any warnings.

The temporary solution is to download the UNIX/Linux version and run it in a command line.

Andrew

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