https://github.com/nylander/parse_mrbayes_ancestral_states

Create FASTA file for ancestral sequence reported in MrBayes v.3
https://github.com/nylander/parse_mrbayes_ancestral_states

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Create FASTA file for ancestral sequence reported in MrBayes v.3

• Host: GitHub
• URL: https://github.com/nylander/parse_mrbayes_ancestral_states
• Owner: nylander
• License: mit
• Created: 2017-09-22T13:28:35.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2022-10-06T15:16:16.000Z (over 3 years ago)
• Last Synced: 2023-10-20T22:08:50.085Z (over 2 years ago)
• Language: Perl
• Size: 298 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# Parse MrBayes Ancestral States

- Last modified: tor okt 06, 2022  05:10

- Johan.Nylander\@{nrm|nbis}.se

The software MrBayes have the capacity of inferring ancestral character states.

The results are summarized in the `.pstat` file. This script parses the MrBayes

output and saves the actual states or sequence, with the highest posterior

probability, as a fasta-formatted file.

## Example 1: Ancestral state estimation for morphological characters

### Step 1. Set up MrBayes to do the ancestral reconstructions

Here is an example [dataset](data/mix.nex) with combined DNA and morphological

data.  When reading the data, the morphological data are automatically assigned

to a separate partition (number 2). We will define one specific node where

ancestral states should be estimated, then tell MrBayes to report the ancestral

states for all characters in partition 2. The `Lset coding=variable` command is

for accounting for coding bias in the morphological data (see the MrBayes

manual for explanation). Also note that with your data, you might want to

change default settings on substitution models, MCMC, etc.

Exectute the following commands in MrBayes:

    #NEXUS

    Begin MrBayes;

        Set autoclose=yes nowarn=yes;

        Execute mix.nex;

        Taxset MyTaxset = Andricus_curvator Andricus_kollari;

        Constraint MyConstraint = MyTaxset;

        Prset topologypr = constraints(MyConstraint);

        Lset applyto=(2) coding=variable;

        Report applyto=(2) ancstates=yes;

        Mcmc nruns=1 nchains=1 ngen=50000 checkpoint=no;

        Sump;

        Quit;

    End;

### Step 2. Parse the output from MrBayes

Run the `parsemb.pl` script with the `.pstat` file as input. The resulting

sequence is written to standard out, while the details about state

probabilities is printed on standard error:

    $ ./parsemb.pl data/mix.nex.pstat

    # MyConstraint

    485	0=6.361512e-01	2=2.980698e-01	1=6.577902e-02	

    486	1=9.579908e-01	0=4.200920e-02	

    487	2=9.909044e-01	0=8.459564e-03	1=6.360484e-04	

    488	1=9.693519e-01	0=2.806066e-02	2=2.587463e-03	

    489	2=9.919600e-01	0=7.198033e-03	1=8.419819e-04	

    490	0=5.094045e-01	2=4.638707e-01	1=2.672478e-02	

    >MyConstraint Ancestral states at node MyConstraint

    012120

Alternatively, if you wish to have the table (tab separated) and fasta in

separate files:

    $ ./parsemb.pl data/mix.nex.pstat > ancestral.fas 2> ancestral.txt

## Example 2: Ancestral sequence estimation

Here we will report the ancestral sequence for a specific node in the tree.

We will use an example [file](data/dna.nex) with DNA data.

### MrBayes commands:

    #NEXUS

    Begin MrBayes;

        Set autoclose=yes nowarn=yes;

        Execute dna.nex;

        Taxset MyTaxset = Andricus_curvator Andricus_kollari;

        Constraint MyConstraint = MyTaxset;

        Prset topologypr = constraints(MyConstraint);

        Report ancstates=yes;

        Mcmc nruns=1 nchains=1 ngen=50000 checkpoint=no;

        Sump;

        Quit;

    End;

### Run the script:

Here we redirect the table to `/dev/null`, and fold the long sequence using the

unix command `fold`:

    $ ./parsemb.pl data/dna.nex.pstat 2> /dev/null | fold

    >MyConstraint Ancestral states at node MyConstraint

    TCTTGGTCCATTCTTGTGTGAGATATACGCTTTACTTGGTTCTCTATTTGGATGTGGCTCCATTTGGACAATGTGTATGA

    TTGCTTTTGATAGGTACAATGTAATAGTGAAAGGTTTGGCTGGGAAGCCCTTAACAATCACCGGTGCAATTATACGCATA

    ATTGGCCTTTGGGTCTGGGCCATTATTTGGACTATTGCGCCAATGTTTGGATGGAATCGGTTTTATGTACCTGAAGGTAA

    CATGACAGCTTGCGGAACTGATTATTTAAGTAAAGACTGGTTCTCGAGGTCTTACATCCTTGTATACAGTATCTTCGTAT

    ACTATATGCCGCTTTTCCTTATCATATACAGTTACTATTTTATCATCTCAGCTGTATCTGCTCACGAAAAAGCAATGCGC

    GAACAGGCCAAAAAGATGAACGTAGCTTCTCTACGTTCATCTGACAATGCAAACACAAGTGCTGAGCATAAACTCGCAAA

    GGTA

**Alternatively**, we may filter the ancestral sequence and say, for example, that

we should only report the states where the posterior probability is above 0.99.

The other states are given as an "unknown" character (default is "`?`", here we

will use `N`):

    $ ./parsemb.pl --cutoff 0.99 --unknown N data/dna.nex.pstat 2> /dev/null | fold

    >MyConstraint Ancestral states at node MyConstraint

    NNNNGGTCCATTCTTGTGTGAGATATACGCTTTACTTGGTTCTCTATTTGGATGTGGCTCCATTTGGACAATGTGTATGA

    TTGCTTTTGATAGGTACAATGTAATAGTGAAAGGTTTGGCTGGGAAGCCCTTAACAATCACCGGTGCAATTATACGCATA

    ATTGGCCTTTGGGTCTGGGCCATTATTTGGACTATTGCGCCAATGTTTGGATGGAATCGGNNNTATGTACCTGAAGGTAA

    CATGACAGCTTGCGGAACTGATTATTTAAGTAAAGACTGGTTCTCGAGGTCTTACATCCTTGTATACAGTATCTTCGTAT

    ACTATATGCCGCTTTTCCTTATCATATACAGTTACTATTTTATCATCTCAGCTGTATCTGCTCACGAAAAAGCAATGCGC

    GAACAGGCCAAAAAGATGAACGTAGCTTCTCTACGTTCATCTGACAATGCAAACACAAGTGCTGAGCATAAACTCGCAAA

    GGTA

## Thanks to

Thanks to Dr. Robin Beck, Univ. Salford, for feature suggestions.

## Licence and copyright

Copyright (c) 2018-2022 Johan Nylander

Permission is hereby granted, free of charge, to any person obtaining a copy

of this software and associated documentation files (the "Software"), to deal

in the Software without restriction, including without limitation the rights

to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

copies of the Software, and to permit persons to whom the Software is

furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all

copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE

AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,

OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE

SOFTWARE.