how to add a new species as outgroup

[Marh32]

Hi,

I just want to add a new species as outgroup, like this, so how can I finish this procedure? I saw you said that the halReplaceGenome can add a new hal file as outgroup. But I just have a fasta genome. So I'm a bit confused about this situation; how should I go about handling it? Thanks in advance for your help.

Best regards, Hao

[glennhickey]

• extract the root ancestor from Cactus.out.hal with hal2fasta
• align this fasta to New_species with cactus into new.hal
• backup new.hal
• rename the root (Anc0) in this new alignment to something unique (if you already have Anc0 in Cactus.out.hal) using halRenameGenomes
• add Cactus.out.hal as a subtree to this new alignment using halAppendSubtree new.hal Cactus.out.hal Anc0 Anc0 --merge (where Anc0 is the root name from Cactus.out.hal and could be Anc00 you can use halStats to check)

Some related documentation https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/progressive.md#updating-alignments

[Marh32]

Ok. Thank you so much