[phylocom-user] problem when running bladj command in phylocom

Steven Kembel steve.kembel at gmail.com
Fri Mar 8 09:57:11 PST 2013


Hi Adina,

> The ages file corresponds to the `wikstrom.ages' from phylocom-4.2 renamed as “ages.ages”.

This file needs to be named "ages" with no filename extension (i.e. not ages.ages or ages.txt).

> Another question. Why when running phylomatic directly from phylocom software (A) the output newick file is different from when I run the phylomatic online tool (B)?

The difference between those two trees is that (A) has branch lengths while (B) does not. If you're generating your phylogeny from either version of phylomatic with a reference tree that does not have branch lengths, you will need to add them yourself (as you are trying to do) using phylocom's blade function plus a table of clade age estimates such as wikstrom.ages.

-Steve


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