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Tag: baseml
TreeSAAP “problem while running tree”
TreeSAAP “problem while running tree” 0 Hello, I have run into an error in TreeSAAP on only some genes. Most are working fine, but some cause TreeSAAP to return the error “There was a problem while running tree: ” and the progress bar has “Opening file progress: File: /home/Programs/TreeSAAP_3.2/rst” and…
How to identify Substitution rate is per time unit in baseml
Dear members, I am new to this world of baseml. I am following the tutorial provided in www.fish-evol.com/mcmctreeExampleVert6/text1Eng.html. However, I am uanble to detect “Substitution rate is per time unit” in my mld file. I am writing baseml.ctl and my output file result below. Please help me how to calculate…
calculate kappa (transition/transversion) for each tree branch
I wish to estimate transition/transversion ratio per each tree branch. I tried PAML baseml but got estimations only for some of the my MSAs. Can someone recommend another way to calculate it? Thanks seqfile = seq treefile = tree outfile = out noisy = 9 0,1,2,3: how much rubbish on…