UGENE Forum - Print Page

UGENE Forum
https://forum.ugene.net/forum/YaBB.pl General Category >> Bugs and Issues >> problem saving MSA file? https://forum.ugene.net/forum/YaBB.pl?num=1306140115 Message started by Poh on May 23^rd, 2011 at 3:41pm

Title: problem saving MSA file?
Post by Poh on May 23^rd, 2011 at 3:41pm

Hi!

I have problem saving and viewing MSA file in ugene 1.9.2.

After generating *aln file from FASTA, clustalw was executed with the file.

A multiple alignment was show, but there is no way to save the file.

After running the tree function to generate the Phylo tree, MSA file were gone.

I need the MSA file to compare against the tree to select a suitable cluster of organism for further work.

Any solution or is it a bug?

Thanks.

Title: Re: problem saving MSA file?
Post by Mikhail Fursov on May 23^rd, 2011 at 4:46pm

Hi!

To save a file you can use either "Save All" option available from "File" menu of main application toolbar or select the file you want to save in Project View and choose "Save selected documents" option.

If either of these options does not work for you, please tell - probably this is a bug.

Title: Re: problem saving MSA file?
Post by Poh on May 24^th, 2011 at 1:19pm

ok it works.

Just that maybe it would make more sense if it is auto saved or just generate the MSA.aln file directly and store somewhere. Usually we would expect a file to be generated and viewed with different tools. But not stored in memory somewhere and to loose if after we close the files.

Thanks!

Title: Re: problem saving MSA file?
Post by Mikhail Fursov on May 24^th, 2011 at 8:02pm

Re-alignning of MSA is a one of a set of MSA editing operations like 'delete symbol', 'reorder', 'insert space'.

Making auto-saving after every op looks overkill here. Once the document is modified it is marked with blue color and asterisk (* sign) is added to the main UGENE window title.
Note, when you close UGENE it will ask you if to save the file modified.