delt0r/msms

Branch length precision

Closed this issue · 3 comments

paula-tataru commented

When using a large population size, the default decimal format "0.00000" for the branch lengths of the marginal trees does not have high enough precision.

For example, for the following command
msms 4 2 -T -t 2.4e6 -r 959999.904 10000000 -eG 0 175028.1728 -eN 1.04167e-6 0.00125
several branches have length 0.

An option should be added to specify the desired precision for the outputted trees.

delt0r commented

There is the -oFP option for just this reason. The format of this format string is identical to java's DecimalFormat.
For example:
msms 20 1 -t 1 -T -oFP 0.000000E00

paula-tataru commented

Thanks. I have to say that I couldn't find anything about this option in any of the 3 docs (CheatSheet, InternalManual and Manual), so you should consider adding a few lines about it.

delt0r commented

You can use msms -help. Its always the most up to date
and authoritative documentation.

On Wed, May 29, 2013 at 5:48 PM, paula-tataru notifications@github.comwrote:

Thanks. I have to say that I couldn't find anything about this option in
any of the 3 docs (CheatSheet, InternalManual and Manual), so you should
consider adding a few lines about it.

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