Adding Multiple Genomes to an Existing Cactus Alignment in a Single Step

[Liuyj-l]

I am using the following command to add a new genome to an existing Cactus alignment:

singularity exec -B /path/ cactus_v2.8.2.sif cactus-update-prepare add branch
--childGenome So
--parentGenome Anc00
--cactus-prepare-options '--alignCores 30'
--outDir ./steps2
--jobStore ./jobstore2
--ancestorName Ancnew1
--topBranchLength 0.001
Tal.hal ./input.txt

I understand that this approach allows a new genome to be added to an existing Cactus alignment, but it seems that only one genome can be added at a time. Is there a way to add multiple new genomes to the alignment in a single step?

[glennhickey]

cactus-update-prepare only supports one genome at a time. You can add alignments together using halAppendSubtree

[Liuyj-l]

Thank you very much for your helpful explanation. I will follow your suggestions and proceed accordingly.
Best regards,
Liuyj