I want to perform a PCA or tree calculation on a rather large aligned sequence file (12,733 sequences). When I do, the program just gets stuck at the step shown below displaying “Calculating tree” without any advancements.
I tried checking the memory use under Tools>show memory usage, and it showed I still had over 80-85% free memory remaining.
I was curious if anyone had similar issues and if there is a strategy or setting I could use to get it done? Thank you so much!
FYI My current Jalview version is 2.11.2.2 on a window OS.
Hi. Jalview is probably still calculating the tree … neighbourjoining is the most computationally taxing tree algorithm jalview provides.
Have you tried the upgma tree option ? This is a bit faster, and good enough for most msa clustering tasks short of evolutionary analysis. Alternatively it might be best to save your alignment to a flatfile, run it through fasttree or another tree calculation tool and import the resultant newick file.
We will be looking to add support for access to phylogeny services in a future jalview release.
Have you considered using an upgma tree? Short of evolutionary analysis, this is a little bit faster and sufficient for the majority of MSA clustering jobs. It might be preferable to save your alignment to a flatfile, run it using fasttree or another tree computation programme, and then import the resulting newick file.
The upgma tree option may be worth a try. With the exception of evolutionary analysis, this is a little faster and adequate for the majority of MSA clustering tasks. As an alternative, it might be advisable to export your alignment to a flatfile, run it via fasttree or another tool for calculating trees, and then import the resulting newick file.
