search

evolbioinfo / goalign

Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language.
GNU General Public License v2.0
73 stars 8 forks source link

Add options to allow partial bootstrap sampling. #8

Closed xiekunwhy closed 3 years ago

xiekunwhy commented 3 years ago

Hi,

Can you add some options to allow users to do partial bootstrap sampling, say that the total length of my sequence is 10Mb, but I just want 1Mb when do bootsraping using goalign build seqboot/distboot.

Best, Kun

fredericlemoine commented 3 years ago

Hi Kun,

I am not sure that resampling with replacement 1Mb over 10Mb will give statistically robust supports (actually there is this partial bootstrap here). Maybe a simple subsampling can solve your problem? (I just added this option: goalign sample sites --consecutive=false on the v0.3.3d release. Let me know what you think.

Best, Frederic

xiekunwhy commented 3 years ago

Hi Frederic,

I just want an alternative tool to realize Jackknife function in phylip-seqboot, not exactly sub-resampling with replacement, jackknife is useful when computation resources and time is limited, and it can avoid some potential problems of bootstrap.

Do you have any plan to add some options or functions to do jackknifle or parametric bootstrap?

Best, Kun

fredericlemoine commented 3 years ago

Hi,

If you think it is useful, you can try to use the option --frac/-f of build seqboot/distboot just implemented in this pre-release. If this answers your question, feel free to close the issue,

Best, Frédéric

xiekunwhy commented 3 years ago

Hi,

Thank you very much, and I am now close it.

Best, Kun