How to perform MrBayes MCMC analysis precisely?

jModelTest suggests set up this models, but MrBayes don´t accept it; neverthless in the paper: Colletotrichum gloeosporioides species complex. Studies in Mycology 13, they used some of those. Thank you for you attention. 

I ran a very long analysis but it was unintensionally interrupted, but I don't want to start over again. If it is possible, how do I do it?

I want to do a phylogeny analysis for forty species from different orders for a protein that has about 500 amino acids. Can someone send me the relevant command line for RAxML and MrBayse software?

Say, nruns=2 nchains=4

I recently ran a Bayesian inference analysis using MrBayes on the CIPRES Science Gateway, but the analysis ran out of time (168 hours). Currently, the analysis is set to 4 runs, 6 chains, 0.7 temperature, 200 million generations on 604 sequences. This is only for the COI region. Is there a way to decrease the time taken for the analysis, for instance, by adding more runs/chains? On the side, I did run the analysis at 50 million generations before, but the split frequency did not stabilize at or close to 0.1. The analysis also has several duplicate entries for some species (roughly 30+ sequences per species) because i was not sure if only 1-2 sequences per species would be enough.

I am running a set of data (DNA coding seqs, alignments done in mega x) in Nexus format. I used mrbayes template (by Barry G hall, Utility program in Mr bayes) to build my block. However, It doesn't execute the block, keeps giving me the error below:

rBayes > exe C:\bin\allseq.bay.txt

Executing file "C:\bin\allseq.bay.txt"

DOS line termination

Longest line length = 5011

Parsing file

Expecting NEXUS formatted file

Reading taxa block

Allocated taxon set

Defining new set of 154 taxa

Expecting '<name> or <number>'

Instead found '|' in command 'Taxlabels'

The error occurred when reading char. 17-17 on line 6

in the file 'C:\bin\allseq.bay.txt'

Returning execution to command line ...

Error in command "Execute"

I can't find the error in character 17-17- line 6!

Any help would be appreciated.

Mah

I checked the web and found no clear definition on how these various statistical methods differ from each other and how they are estimated. Could anyone elaborate a little bit?

Any suggestions on which software to use and I would like to know if I can use aligned gene sequences in FASTA format and then concatenate or first concatenate all the genes and then align for different species and use for phylogeny.

Hi All,

I am working with mtDNA and want to know how I can determine burn-in generation and number of chain in MrBayes and other Bayesian inference software?

thanks

Hossein