Asked 19th Nov, 2017

Can anyone suggest am alternative to SDSC biology workbench? Either open source or cheap license?

sdsc biology workbench has been shut down. I am desperate to find sequence analysis tool that will help me

Most recent answer

9th Jun, 2019
John Jungck
University of Delaware
For beginners try DNA Subway:
1 Recommendation

All Answers (5)

20th Nov, 2017
Matej Lexa
Masaryk University
Dear Rasika,
I assume you are looking for a "point-and-click" user interface as opposed to environments like Bioconductor, Biopython or Biopieces where you have to work on the command line mostly.
In a way, Taverna ( and Galaxy ( may be good replacements. They are both powerful "workflow management tools" with some kind of graphical user interface, but perhaps not as easy to use as The SDSC Biology Workbench.
If you need something simple and don't mind copying and pasting data via the clipboard, the Sequence Manipulation Site ( and EBI Services web collection ( could be useful.
Invest on local infrastructure - can be started with simple 1 computer - Biolinux with
1) use python, bioconda
2) use R + bioconductor
and combine with open source tools like
EBI Services web tools -
MPI Bioinformatics toolkit -
Sequence Manipulation Site -
21st Nov, 2017
Rasika Mudalige
University of Dubuque
Thank you for both of your suggestions. I tried the Genome workbench. It is a learning curve and I am still at the very beginning. But I am getting the hang of it. Thank you to both of you.
29th Nov, 2018
Carlos E Alvarez
The Ohio State University Colleges of Medicine & Veterinary Medicine
I think most or all tools in the SDSC Biology Workbench are individually freely available, but I'm not aware of a similar server environment with all the tools and a user account for storing data/results. If you are still looking for the basic tools at one site, I recommend ENSEMBL-EBI:
9th Jun, 2019
John Jungck
University of Delaware
For beginners try DNA Subway:
1 Recommendation

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Any advice for using PAML to estimate dn/ds for 4 sequences only?
8 answers
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I am so incredibly confused by PAML. Over the last week I've read what feels like half the internet to get a good grasp on how to use it. I'm still stuck, despite using a combination of different codeml.ctl file layouts to try and dig into my problem.
My problem is that I only have 4 sequences for each gene I am looking at. Two of these sequences are from the same species, and I want to look at whether their dns/ds ratios vary (either site specific or branch specific). The other two sequences are quite distantly related.
I have asked both the null hypothesis and an alternative for the whole tree, and the omega's are significantly different, which means that there are different omegas over the tree.
I then have tried to label the split between my species of interest as #1, and calculate a dn/ds specific to those two branches. The more I look at them, the more I think I should be using a ML method to compare the two.
Is the case simply that my original 4 sequences are too divergent, and I can't ask anything using PAML, and will need to use a different method (such as HYPHY?)?
Or am I overlooking something in my output that should be telling me what I'm looking to know? Or asking the wrong questions in the first place.
I see suggestions for attaching the codeml.ctl file you are using to help with the troubleshooting, but honestly so far I have tried such a variety (with setting/estimating omega values, using different models (0, 1, 2)  and trying to vary the NSsites (0, 2, 7, 8).
My supervisor is suggesting that I follow the methods of two other papers, but both use more sequences and are more closely related to the outgroups.

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