Using Mr Bayes to For Phlyogenetic Analysis - Revision history

Davebrid: changed instructions for burnin

2009-09-13T14:42:20Z

changed instructions for burnin

← Older revision		Revision as of 14:42, 13 September 2009
Line 10:		Line 10:
	#Type '''lset nst=6 rates=invgamma'''. This is for nucleotide, for protein use '''prset aamodelpr=mixed'''		#Type '''lset nst=6 rates=invgamma'''. This is for nucleotide, for protein use '''prset aamodelpr=mixed'''
	#Type '''mcmc ngen=10000 samplefreq=10'''. If the average standard deviation is below 0.01 then type no to continue. Else type yes until it reaches this threshold.		#Type '''mcmc ngen=10000 samplefreq=10'''. If the average standard deviation is below 0.01 then type no to continue. Else type yes until it reaches this threshold.
	#Type '''sump burnin=250''', where 250 is 25% of your generations. For example if you ran 10 000 generations (sampled 1000 generations, you would use 250). Check that the potential scale reduction factor (PSRF) is close to 1.0 for all samples. If it is not run some more generations		#Type '''sump burnin=250''', where 250 is 25% of your generations. For example if you ran 10 000 generations (sampled every tenth for 1000 generations sampled) you would use 250. Check that the potential scale reduction factor (PSRF) is close to 1.0 for all samples. If it is not run some more generations
	#Type '''sumt burnin=250''', where 250 is the same parameter as above. This will output both a cladogram and a tree file		#Type '''sumt burnin=250''', where 250 is the same parameter as above. This will output both a cladogram and a tree file
	#Transfer all files into another directory for saving.		#Transfer all files into another directory for saving.
			#View tree using TreeView

Davebrid at 12:42, 10 September 2009

2009-09-10T12:42:01Z

← Older revision		Revision as of 12:42, 10 September 2009
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	#Type '''mcmc ngen=10000 samplefreq=10'''. If the average standard deviation is below 0.01 then type no to continue. Else type yes until it reaches this threshold.		#Type '''mcmc ngen=10000 samplefreq=10'''. If the average standard deviation is below 0.01 then type no to continue. Else type yes until it reaches this threshold.
	#Type '''sump burnin=250''', where 250 is 25% of your generations. For example if you ran 10 000 generations (sampled 1000 generations, you would use 250). Check that the potential scale reduction factor (PSRF) is close to 1.0 for all samples. If it is not run some more generations		#Type '''sump burnin=250''', where 250 is 25% of your generations. For example if you ran 10 000 generations (sampled 1000 generations, you would use 250). Check that the potential scale reduction factor (PSRF) is close to 1.0 for all samples. If it is not run some more generations
	#Type '''~~sump~~ burnin=250''', where 250 is the same parameter as above. This will output both a cladogram and a tree file		#Type '''sumt burnin=250''', where 250 is the same parameter as above. This will output both a cladogram and a tree file
	#Transfer all files into another directory for saving.		#Transfer all files into another directory for saving.

Davebrid at 19:35, 9 September 2009

2009-09-09T19:35:27Z

← Older revision		Revision as of 19:35, 9 September 2009
Line 8:		Line 8:
	#May need to edit the file to remove the line defining symbols.		#May need to edit the file to remove the line defining symbols.
	#Type '''execute filename.exe''' with your filename specified		#Type '''execute filename.exe''' with your filename specified
	#Type '''lset nst=6 rates=invgamma'''		#Type '''lset nst=6 rates=invgamma'''. This is for nucleotide, for protein use '''prset aamodelpr=mixed'''
	#Type '''mcmc ngen=10000 samplefreq=10'''. If the average standard deviation is below 0.01 then type no to continue. Else type yes until it reaches this threshold.		#Type '''mcmc ngen=10000 samplefreq=10'''. If the average standard deviation is below 0.01 then type no to continue. Else type yes until it reaches this threshold.
	#Type '''sump burnin=250''', where 250 is 25% of your generations. For example if you ran 10 000 generations (sampled 1000 generations, you would use 250). Check that the potential scale reduction factor (PSRF) is close to 1.0 for all samples. If it is not run some more generations		#Type '''sump burnin=250''', where 250 is 25% of your generations. For example if you ran 10 000 generations (sampled 1000 generations, you would use 250). Check that the potential scale reduction factor (PSRF) is close to 1.0 for all samples. If it is not run some more generations
	#Type '''sump burnin=250''', where 250 is the same parameter as above. This will output both a cladogram and a tree file		#Type '''sump burnin=250''', where 250 is the same parameter as above. This will output both a cladogram and a tree file
	#Transfer all files into another directory for saving.		#Transfer all files into another directory for saving.

Davebrid: wrote initial page

2009-09-09T19:22:22Z

wrote initial page

New page

==Software==
*Mr Bayes for detailed instructions see the [http://mrbayes.csit.fsu.edu/wiki/index.php/Tutorial#Quick_Start_Version manual]
*Sequence Alignment Software (CLUSTALX or MUSCLE)

==Analysis==
#Generate sequence alignment and save as a nexus formatted file.
#Move file to Mr Bayes directory
#May need to edit the file to remove the line defining symbols.
#Type '''execute filename.exe''' with your filename specified
#Type '''lset nst=6 rates=invgamma'''
#Type '''mcmc ngen=10000 samplefreq=10'''. If the average standard deviation is below 0.01 then type no to continue. Else type yes until it reaches this threshold.
#Type '''sump burnin=250''', where 250 is 25% of your generations. For example if you ran 10 000 generations (sampled 1000 generations, you would use 250). Check that the potential scale reduction factor (PSRF) is close to 1.0 for all samples. If it is not run some more generations
#Type '''sump burnin=250''', where 250 is the same parameter as above. This will output both a cladogram and a tree file
#Transfer all files into another directory for saving.