https://github.com/nylander/remove_mcmc_output

Remove all those files generated by phylogenetic MCMC software
https://github.com/nylander/remove_mcmc_output

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Remove all those files generated by phylogenetic MCMC software

• Host: GitHub
• URL: https://github.com/nylander/remove_mcmc_output
• Owner: nylander
• License: mit
• Created: 2013-10-02T15:01:05.000Z (over 12 years ago)
• Default Branch: main
• Last Pushed: 2025-05-15T12:53:51.000Z (about 1 year ago)
• Last Synced: 2025-12-04T09:57:58.008Z (6 months ago)
• Language: Shell
• Size: 6.84 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# remove_mcmc_output

Remove all those files generated by phylogenetic MCMC software.

## Description

Running a MCMC program (e.g., [MrBayes](https://github.com/NBISweden/MrBayes),

[BEAST2](https://github.com/CompEvol/beast2),

[PhyloBayes](https://github.com/bayesiancook/phylobayes)) often generates a

large number of files. If you wish to repeat your analyses in the same working

directory, you either need to make sure files are overwritten, named something

else, or simply remove them before the next run.

The provided scripts ([`rmbayes`](rmbayes), [`rmbeast`](rmbeast),

[`rmphylobayes`](rmphylobayes)), attempts to remove all those files generated by

the software, while keeping the original data. Please make sure to look at the

list of files to be removed before deleting them!

## Options

- `-h`, `--help`  Show help text

- `-v`, `--version`  Show version number

- `-f`, `--force`  Delete found files without asking

Default (no options) is to remove interactively (answering "y" or "n").

## Example: Removing all output from a MrBayes run

    $ rmbayes

    Found the following output from MrBayes

    ./lw.nex.ckp

    ./lw.nex.ckp~

    ./lw.nex.con.tre

    ./lw.log

    ./lw.nex.lstat

    ./lw.nex.mcmc

    ./lw.nex.run2.p

    ./lw.nex.run1.p

    ./lw.nex.parts

    ./lw.nex.pstat

    ./lw.nex.run2.t

    ./lw.nex.run1.t

    ./lw.nex.trprobs

    ./lw.nex.tstat

    ./lw.nex.vstat

    Do you want to delete these files [y/n]? y

    removed './lw.nex.ckp'

    removed './lw.nex.ckp~'

    removed './lw.nex.con.tre'

    removed './lw.log'

    removed './lw.nex.lstat'

    removed './lw.nex.mcmc'

    removed './lw.nex.run2.p'

    removed './lw.nex.run1.p'

    removed './lw.nex.parts'

    removed './lw.nex.pstat'

    removed './lw.nex.run2.t'

    removed './lw.nex.run1.t'

    removed './lw.nex.trprobs'

    removed './lw.nex.tstat'

    removed './lw.nex.vstat'

### Notes

- If you wish to live dangerously, you may use `rmbayes -f` or simply

  say `yes | rmbayes`!

- Some software packages evolve rapidly, so the list of files searched for by

  the provided script may not be entirely up to date.

### Copyright and License

[MIT License](LICENSE)

### Download