1 / 5

Demo: MrBayes

Demo: MrBayes. http://mrbayes.csit.fsu.edu/ http://abacus.gene.ucl.ac.uk/ziheng/teach/testMB.nex Ziheng Yang Department of Biology, UCL. Small example file. http://abacus.gene.ucl.ac.uk/ziheng/teach/testMB.nex. MrBayes commands. exec : loads a file and run commands in it

sagira
Download Presentation

Demo: MrBayes

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Demo: MrBayes http://mrbayes.csit.fsu.edu/ http://abacus.gene.ucl.ac.uk/ziheng/teach/testMB.nex Ziheng Yang Department of Biology, UCL

  2. Small example file http://abacus.gene.ucl.ac.uk/ziheng/teach/testMB.nex

  3. MrBayes commands exec: loads a file and run commands in it lset: sets the substitution model prset: sets the prior mcmcp: sets parameters for the mcmc. mcmc: same as mcmcp but starts mcmc as well. sump: summarizes parameters sumt: summarizes trees (ignore branch lengths) quit: return to OS.

  4. MrBayes data block #NEXUS begin data; dimensions ntax=5 nchar=30; format datatype=dna missing=? gap=-; matrix A AATAGAGTGA GACCATTAGG CACTAAACTA B AAACGAGTGA GACGATTAGT CACAAAGATA C AAGCGATTCA GACAGTTAGC CACAAATGTA D AATTGAATCA GACAATGAGC CACCAATATA E AAGTGATTCA GTCAGTGAGT CACTAATTTA ; end;

  5. MrBayes command block begin mrbayes; lset nst=2 ; mcmcp ngen=1000000 samplefreq=1000 printfreq=10000; mcmcp nchain=2 burnin=2000; mcmc; sumt; sump; end;

More Related