[Jalview-discuss] Sort by tree order

[James Procter]

Hi Sebastien.

Sebastien MORETTI wrote:
> we use this parameter for the applet and it does what it should:
>     <param name="sortBy"           value="Tree Order" />
> 
> But this value does not seem to exist.
It seems you are correct there!  I just checked the V2.4 source
thoroughly, and that value of the sortBy parameter will have no effect.

> Maybe it resets some internal parameters but our multiple sequence
> alignment is build from a guide tree which in most cases has the same
> topology than our phylogenetic tree (Only branch lengths are different)
> 
> So, this value allows us to keep the same order than the guide tree and
> in most cases than the phylogenetic tree.

For most multiple sequence alignment programs, the guide tree would tend
to reflect the final alignment ordering and since JalviewLite will not
re-order the alignment unless a valid sortby parameter is provided, the
displayed ordering is always as specified in the alignment file.

Jim.

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