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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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Cactus input tree #1303

Open zhxh233 opened 6 months ago

zhxh233 commented 6 months ago

Hi,

I ran into trouble when running with my own dataset. As asked in other issues, Cactus asks the branch length of input tree as substitution rate, however I have only 2 trees with branch lengths in terms of time(Myr) or diversification rate (species/Myr). If I plan to build my own tree to bypass this issue( as in the doc, using mashtree or IQ tree), should I use whole-genome infromation or partial sequences as in the ref (where I got the 2 trees mentioned above) ?

Many Thanks for your help. XH

glennhickey commented 6 months ago

I suggest using the same data to build the tree as you want to align, if possible. So if you are aligning whole genomes, then use whole genomes to make the tree.

zhxh233 commented 6 months ago

Thanks! I'll try it : )