Failing to conduct tree or PCA calculation on large alignment file


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 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.

I will give your suggestions a shot! Thank you so much.

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.