Splitting up a Sequencing Project into Sub Projects

You can split up a sequencing project into sub projects either by exporting selected sequences using the menu option 'File' -> 'Export Selected Sequences' -> 'to a new alignment window'

OR

by using menu options 'File' -> 'Split/Export Alignment/Sequences By Name Groups'.

The 'Split' option is described here

the 'Split' function divides a project up based on the names of the sequences in the alignment

eg if you had 7 sequences in an alignment named as follows

SAMPLE1_F1
SAMPLE1_R1
SAMPLE2_F1
SAMPLE2_R1
SAMPLE3_F1
SAMPLE3_R1
SAMPLE3_R2

and you used the 'Split' function with the delimiter set as '_' (which is the default)

the alignment would be split between three new windows as follows...

window1 containing sequences SAMPLE1_F1 and SAMPLE1_R1
window2 containing sequences SAMPLE2_F1 and SAMPLE2_R1
window3 containing sequences SAMPLE3_F1 and SAMPLE3_R1 and SAMPLE3_R2

ie new projects are formed from sequences that have identical characters to the left of the set delimiter character in the sequences names

Split Options

You can either split an alignment and 'retain' the existing gaps etc, or you can opt to 're-align' the sequences within each new sub-project as it is formed. You should note that if you use the 're-align' option, it's possible that DNADynamo won't be able to re-add every sequence to a sub-project, if some of the sequences don't form a high scoring alignment within the project.