No, I'm afraid Geneious doesn't support exporting modified .abi files.

If contig assembly is your thing and you haven't already, may I suggest you try out the Geneiou 4.8 beta (up on the website) which includes a bunch of improvements in this area especially de novo assembly.

Hi Aks0126,

Could you tell me what it is you need to do in Sequencher? If you let us know, we would be happy to show you how this is possible in Geneious.

We have many Sequencher projects including those where original data was edited. It is costly and inefficient to use both Sequencher and Geneious, and Geneious allows for better organization and processing of data. A .CAF file may be exported from Sequencher and imported into Geneious, but doing this one-by-one would take forever. Is there some automated method (script?) that would allow us to move all Sequencher projects into Geneious? If not, we will be forced to continue using Sequencher.

The problem is the Sequencher Project Files which are proprietary binary files and the Sequencher license forbids reverse engineering it so it isn't possible for us to write an importer. This is why we went with the CAF format since it is open and Sequencher supports export. However, to get data from SPF format into CAF you have to use a tool that understands the project format (i.e. Sequencher) and it isn't in their interests to make batch exporting easy otherwise they wouldn't be able to maintain their lock-in.

Sorry we can't be more help,

Shane

I am attempting to import my sequencher data in using the CAF files. Sometimes it works and other times I get the error: "The read 'some sequence name' lies outside the contig" What does this mean and is there a fix for it?

Also, when importing fasta files exported from sequencher, if the sequence has a gap sequencher codes it as ':'. But it seems that geneious won't recognize the ':' and doesnt know how to import the file a sequence. Is there an efficient way around this without having to do a find/replace in each of the sequencher exported fasta files?

Sequencher has proven to be somewhat buggy in its CAF export but there have also been bugs in our CAF import. The easiest way to fix these is for you to send any problematic files to us at support@biomatters.com and we can have a look and see where the issue is.

For your FASTA files, I would normally use a typical UNIX command like sed to do a rapid search and replace of the ':' characters with '-'. Otherwise, you'll probably need to use some other text editor (not MS Word which is a word processor rather than a text editor).

Shane

I would like to echo Shane's request for anyone having trouble importing their CAF files to send us examples of files that won't import to help us improve our importer.

I would also like to mention that Geneious now supports the export of modified .ab1 files which you can import into Sequencher (or anyhting else)