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ma-compbio / Phylo-HMRF

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Can Phylo-HMRF do pairwise comparison? #5

Open llq0325 opened 4 years ago

llq0325 commented 4 years ago

Hi, Very delicacy approach Phylo-HMRF has! I would like to try it in my research. I have a question though, can Phylo-HMRF do comparison between two species? and how can I do it?

cheers.

yangymargaret commented 4 years ago

Hi @llq0325, Thank you very much for your interest in Phylo-HMRF and thank you for the question. Yes, Phylo-HMRF can perform comparison between two species. In this case, the phylogenetic tree is simplified to be a tree with four nodes: one remote ancestor node (root node), one ancestor node, and two leaf nodes (representing the two species to study). Please edit the input files edge.1.txt, branch_length.1.txt, and species_name.1.txt accordingly. Please see the README about how to prepare the input files and the input data. Please let me know if you have any other questions. Thanks!

Best regards! Yang Yang

llq0325 commented 4 years ago

Hi Yang,

Thank you for replying. In current version of utility.py, you hard code the species name list. Maybe you can consider leave them out for a wider use. https://github.com/ma-compbio/Phylo-HMRF/blob/b20f4e901d66f08de5a6d65b0d693583147f5236/utility.py#L2476

regards,

Langqing

yangymargaret commented 4 years ago

Hi Langqing @llq0325 , Thank you very much for letting me know this problem. I have updated utility.py accordingly. Please let me know if you have any other questions. Many thanks!

Best regards! Yang Yang