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minor formatting, typos
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Don86 committed May 31, 2018
1 parent d9da29e commit a3bbe4f0695bc937577eb7599f42890f688640d8
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  1. +4 −3 content/mrbayes_quickstart.md
@@ -4,14 +4,14 @@ _(Mostly a condensed verion of the quickstart already in the official manual, or

### Overview

* Uses a variant of MCMC (with "hot" and "cold" chains - see the **MCMC Chains** section below) to produce a file with multiple trees <extension `.t`). Does not produce time-resolved trees.
* Uses a variant of MCMC (with "hot" and "cold" chains - see the **MCMC Chains** section below, under "**Other Useful Stuff**") to produce a file with multiple trees (extension `.t`), and a log file (extension `.p`). Does not produce time-resolved trees.
* Pretty fast for an MCMC-based tree algorithm (faster than BEAST, anyway).
* Can do other kinds of analysis like dNdS, with HPD intervals.
* Doesn't like special characters - will convert them all to underscores. This is highly annoying.

## 1. Quickstart

There are two modes of operation: interactive mode and batch mode. The interactive mode is initialized just by typing `mb` into the command line, after which you'll enter parameter inputs line by line, and in batch mode, you'll prepare a text file containing all the necessary parameters, and simply run that text file with `mb my_run_file.txt`. This tutorial assumes that you already have a suitable input `.nexus` file containing your aligned sequences.
There are two modes of operation: interactive mode and batch mode. The interactive mode is initialized by typing `mb` into the command line, after which you'll enter parameter inputs line by line. In batch mode, you'll prepare a text file named, say, `my_run_file.txt` containing all the necessary parameters, then run that text file using `mb my_run_file.txt`. This tutorial assumes that you already have a suitable input `.nexus` file containing your aligned sequences.

### Interactive mode

@@ -28,6 +28,7 @@ To break that down:
* `set usebeagle=yes beagledevice=gpu beagleprecision=single;` - Use the BEAGLE GPU library. Use single-precision for less accurate, but marginally faster runs. There's a BEAGLE SSE option as well, which doesn't help with single-precision runs, but could help speed up double-precision runs (not tested yet)
* `execute input_file.nexus;` - Loads the input file, in nexus format.
* `lset nst=6 rates=gamma;`- Use the GTR model, with gamma priors. Use `help lset` in interactive mode to see more options.
* `mcmc...` - mcmc parameters: 1 run, 2 chains, 10M chain length, sampling every 10,000 states (to get 1,000 trees). The "cold" and "hot" chains may swap positions every 100,000 states; specified by the `diagnfreq` parameter.

### Batch mode

@@ -105,4 +106,4 @@ The default setting for `mrbayes` is to have 2 runs, each with 4 chains (3 hot,
### Useful Links

* [1] [Wikipedia article](https://en.wikipedia.org/wiki/Bayesian_inference_in_phylogeny) on MCMCMC
* Tim Vaughan's Bayesian MCMC [lecture slides](https://tgvaughan.github.io/BayesianMCMCLectures/)
* [2] Tim Vaughan's Bayesian MCMC [lecture slides](https://tgvaughan.github.io/BayesianMCMCLectures/)

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