ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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Help parameterizing seqfile #1437

Open desmodus1984 opened 4 months ago

desmodus1984 commented 4 months ago

Hi, I am interested in using ragout to scaffold a bat genome that I am sequencing. To run it I need to align it with other genome assemblies for scaffolding. I wanted to inquire about parameterizing the seqfile. I need a phylogenetic tree, and I created one:

((HLmolMol,((HLmyoMyo,Myosep),HLpipKuh)),(HLrhiFer,HLrouAeg));

My question is how to determine or to estimate the branch lengths.

For example, there is a paper that created a tree with all the 21 families of bats, but there are only reference-based genome assemblies for six species from six families. https://onlinelibrary.wiley.com/doi/10.1111/1749-4877.12772 A molecular phylogeny for all 21 families within Chiroptera (bats)

Could you help how to estimate the branch lengths.

In addition, I couldn't find any requirements, which I thought cactus had before; thus I only need the precompilled binaries to run cactus now?

Thanks;

glennhickey commented 4 months ago

Here's a new tool to compute trees and branch lengths. Give it a try:

https://github.com/TurakhiaLab/ROADIES